Using Longitudinal MRI to Manage Proton Range Uncertainty for Pediatric Proton Craniospinal Irradiation

PURPOSE/OBJECTIVE(S)

Clinical evidence has shown that proton therapy can effectively reduce side effects for pediatric patients undergoing vertebral body-sparing craniospinal irradiation (VBS CSI), compared to conventional photon treatment modalities. However, radiation-induced growth impairment remains challenging for VBS CSI due to proton range uncertainty, compromising vertebral body sparing for growing children. Previous studies have shown that fatty marrow replacement can be observed in vertebral bodies 4-48 weeks after treatment is complete. This study aims to detect and quantify the fatty marrow replacement in vertebral bodies using longitudinal magnetic resonance (MR) to manage proton range uncertainty.

MATERIALS/METHODS

A prospective clinical trial of proton VBS CSI was designed, and ten pediatric patients were enrolled with prescribed doses of 15-36 Gy. The thecal sac and neural foramina were the clinical target volumes, and a Monte Carlo planning system was used to robustly optimize treatment plans with a 3.5% range margin. We analyzed patients' T1/T2 MR images acquired before, during, and after proton treatment to investigate the hematopoietic marrow transformation induced by irradiation. A metric was defined to calculate the ratio of fatty and hematopoietic marrow based on relative MR intensity histograms. We proposed a machine learning method via Gaussian fitting process (ML-GFP) to explore hidden correlations between marrow transition and radiation dose to 2 cm3 of the bone marrow (D2cc). We also leveraged this method to embed uncertainty to support potential proton range management for VBS enhancement.

RESULTS

The results indicated that fatty marrow replacement could be observed during inter-fractional treatment. For instance, an individual patient showed that the fatty marrow generation ratios were 0.54, 0.74, and 0.45, corresponding to 11, 18, and 65 days after the treatment started. Using ML-GFP, the fatty marrow transition was found to be quadratically correlated to treatment fractions, and the maximum transformation ranged from 40 to 50 days. Then marrow regeneration was observed due to the decrease in fatty marrow ratios. The fatty marrow ratios were also positively correlated to the D2cc doses ranging from 10 Gy to 36 Gy. Limited by insufficient low-dose data, the ML-GFP model extrapolated the data to predict the marrow transformation below 10 Gy.

CONCLUSION

We demonstrated the feasibility of using non-invasive longitudinal MR to quantify the fatty marrow transition from inter-fractional treatment. Based on this prospective study, the method can detect early fatty marrow generation in vertebrae caused by proton irradiation due to the conservative range margin used for robust optimization. The proposed method could be used to validate the actual proton range, allowing an accurate range margin to be defined to preserve bone marrow. Future investigation will likely focus on clinical implementation to improve life quality for pediatric CSI patients.

Estimating Potential Benefits of Online Adaptive Proton Therapy for Head-and-Neck Cancer: A Retrospective Study

PURPOSE/OBJECTIVE(S)

Proton therapy is highly sensitive to anatomical changes and setup variations in head-and-neck (HN) treatments. To address this issue, proton centers often acquire patient CT images weekly to monitor patient anatomical changes during the treatment course and perform offline plan adaptation when needed. However, offline adaptation cannot fully account for daily setup variations or the anatomical changes occurring with high frequency. There are a few groups endeavoring to develop advanced technologies to enable online adaptive proton therapy (APT). However, the necessity of online APT remains controversial, as it is unknown that whether online APT will significantly improve treatment quality and outcomes compared to offline APT. The purpose of this study is to estimate the clinical potential of online APT in the management of HN cancers in relation to the current offline APT.

MATERIALS/METHODS

Our retrospective study was conducted with four HN patients (35 fractions per patient), who had been treated with intensity modulated proton therapy and had offline adaptation once or twice during their treatment courses. Synthetic CT (sCT) images were generated from 140 daily CBCT images for us to recalculate the dose of the treatment plan in patient's actual treatment anatomy for each treatment fraction and adapt the plan when warranted. These adaptations were assumed to be performed online before treatment delivery to mimic an online APT course. Accumulative doses were calculated for both courses using the CBCT-based sCT images of every fraction for us to compare the target coverage, organ at risk (OAR) sparing, tumor control probability (TCP) and normal tissue complication probability (NTCP). An in-house script was developed to semi-automate this process in a commercial treatment planning system to facilitate our study.

RESULTS

All patients would benefit from online APT to different extents. For the first patient, with OAR doses comparable to the actual offline course, the retrospective online APT course improved dose coverages of the three CTVs from 95.2%, 98.64% and 89.53% to 98.88%, 99.81%, 98.97%, which would lead to a 4.52% improvement in TCP. Similarly, online APT would yield a 2.66% improvement in TCP for the second patient. For the third patient, with comparable CTV dose coverages, the mean doses of right parotid and oral cavity were decreased from 29.52 Gy relative biological effectiveness (RBE) and 41.89 Gy RBE to 22.16 Gy RBE and 34.61 Gy RBE, leading to a reduce of 1.67% and 3.40% in NTCP. The mean dose of right parotid was decreased from 21.71 Gy RBE to 19.37 Gy RBE for the last patient, leading to a reduce of 0.73% in NTCP.

CONCLUSION

Our results showed that online APT could better maintain the treatment plan quality than offline APT for all the four patients, despite their significant anatomical changes. Future investigation will focus on collecting more patient data to obtain statistically significant results and help identify the patients to whom the online APT will be of most benefit.

Prediction of plan adaptation in head and neck cancer proton therapy using clinical, radiographic, and dosimetric features

PURPOSE

Because proton head and neck (HN) treatments are sensitive to anatomical changes, plan adaptation (re-plan) during the treatment course is needed for a significant portion of patients. We aim to predict re-plan at plan review stage for HN proton therapy with a neural network (NN) model trained with patients' dosimetric and clinical features. The model can serve as a valuable tool for planners to assess the probability of needing to revise the current plan.

METHODS AND MATERIALS

Mean beam dose heterogeneity index (BHI), defined as the ratio of the maximum beam dose to the prescription dose, plan robustness features (clinical target volume (CTV), V100 changes, and V100 > 95% passing rates in 21 robust evaluation scenarios), as well as clinical features (e.g., age, tumor site, and surgery/chemotherapy status) were gathered from 171 patients treated at our proton center in 2020, with a median age of 64 and stages from I-IVc across 13 HN sites. Statistical analyses of dosimetric parameters and clinical features were conducted between re-plan and no-replan groups. A NN was trained and tested using these features. Receiver operating characteristic (ROC) analysis was conducted to evaluate the performance of the prediction model. A sensitivity analysis was done to determine feature importance.

RESULTS

Mean BHI in the re-plan group was significantly higher than the no-replan group (p < .01). Tumor site (p < .01), chemotherapy status (p < .01), and surgery status (p < .01) were significantly correlated to re-plan. The model had sensitivities/specificities of 75.0%/77.4%, respectively, and an area under the ROC curve of .855.

CONCLUSION

There are several dosimetric and clinical features that correlate to re-plans, and NNs trained with these features can be used to predict HN re-plans, which can be used to reduce re-plan rate by improving plan quality.

Comparison of the early development of the professional values for nursing students in the traditional program and the second-degree program: a longitudinal study

Aim

This study aims to compare the early development of professional value between the students in the traditional programme (BSN) and those in the accelerated BSN (ABSN) programmes.

Design

A longitudinal design was conducted.

Methods

Data were collected from three schools of nursing during one academic year. A total of 117 BSN students and 101 ABSN students completed the survey of demographic information and the Nurses’ Professional Values Scale–Revised questionnaires. All data were analysed by IBM SPSS‐Statistics 22.

Results

Results showed that, in the beginning of the first professional nursing course, both students in the BSN and the ABSN programmes reported similar level of professional values. However, after one academic year, the changes in the professional value varied both between these two programmes and among the three different nursing schools. The increased professional value in school A represented the possibility for students to improve during their first‐year professional nursing programme. As educators, we should redesign our teaching strategies according to the different conditions of students in each programme.

Nanoconfinement of metal oxide MgO and ZnO in zeolitic imidazolate framework ZIF-8 for CO2 adsorption and regeneration

Microporous materials exhibit fast CO₂ adsorption rate with possible sacrificed capacity, while CO₂ chemisorption on metal oxides is remarkable but kinetics and reactive area are critical. In order to adopt the advantages of both microporous sorbent zeolitic imidazolate framework (ZIF) and metal oxide (MO), in this research, magnesium oxide (MgO) and zinc oxide (ZnO) were doped to ZIF-8 (MO@ZIF) using infiltration and calcination processes. The powder X-ray diffraction patterns showed retained ZIF-8 integrity after MO addition. Broad MgO peaks implied well-dispersed nanoparticles, while sharp ZnO diffractions indicated oxide agglomeration, supported by the field emission transmission electron microscope images. ZIF pore size was expanded due to confined MgO without sacrificing the framework porosity. Because of nanoconfinement, the MgO@ZIF-8 room temperature CO₂ adsorption, as well as the adsorption rate constant in pseudo-second order model, were two-fold higher than expectation. In addition, the decarbonation temperature in MgO@ZIF-8 was reduced by 40 degrees. In general, it was found that metal oxide nanoconfinement in microporous zeolitic imidazolate frameworks performed improved CO₂ uptake, facilitated adsorption kinetics at ambient temperature, and lowered regeneration temperature to release CO₂.

DUSP22 suppresses prostate cancer proliferation by targeting the EGFR-AR axis

Dual-specificity phosphatases (DUSPs) regulate the activity of various downstream kinases through serine or threonine or tyrosine dephosphorylation. Loss of function and aberrant expression of DUSPs has been implicated in cancer progression and poor survival, yet the function of DUSP22 in prostate cancer (PCa) cells is not clear. Gene Expression Omnibus and cBioPortal microarray database analyses showed that DUSP22 expression was lower in PCa tissues than normal prostate tissues, and altered DUSP22 expression was associated with shorter progression-free and disease-free survival of patients with PCa. Exogenous DUSP22 expression in LNCaP, PC3, and C4-2B PCa cells inhibited cellular proliferation and colony formation, supporting a growth inhibitory role for DUSP22 in PCa cells. DUSP22 expression significantly attenuated epidermal growth factor (EGF) receptor (EGFR) and its downstream ERK1/2 signaling by dephosphorylation. However, DUSP22 failed to suppress the growth of CWR22Rv1 and DU145 cells with elevated phosphorylated (p-)ERK1/2 levels. A serine-to-alanine mutation at position 58, a potential ERK1/2-targeted phosphorylation site in DUSP22, was sufficient to suppress growth of CWR22Rv1 cells with elevated p-ERK1/2 levels, suggesting a mutually antagonistic relationship between DUSP22 and ERK1/2 dependent on phosphorylation status. We showed that DUSP22 can suppress prostate-specific antigen gene expression through phosphatase-dependent pathways, suggesting that DUSP22 is an important regulator of the androgen receptor (AR) in PCa cells. Mechanistically, DUSP22 can interact with AR as a regulatory partner and interfere with EGF-induced AR phosphorylation at Tyr534, suggesting that DUSP22 serves as a crucial suppressor of both EGFR and AR-dependent signaling in PCa cells via dephosphorylation. Our findings indicate that loss of function of DUSP22 in PCa cells leads to aberrant activation of both EGFR-ERKs and AR signaling and ultimately progression of PCa, supporting the potential for novel therapeutic design of harnessing DUSP22 in the treatment of PCa.-Lin, H.-P., Ho, H.-M., Chang, C.-W., Yeh, S.-D., Su, Y.-W., Tan, T.-H., Lin, W.-J. DUSP22 suppresses prostate cancer proliferation by targeting the EGFR-AR axis.

The Impact of the Shallow-Trench Isolation Effect on Flicker Noise of Source Follower MOSFETs in a CMOS Image Sensor

The flicker noise of source follower transistors is the dominant noise source in image sensors. This paper reports a systematic study of the shallow trench isolation effect in transistors with different sizes under high temperature conditions that correspond to the quantity of empty defect sites. The effects of shallow trench isolation sidewall defects on flicker noise characteristics are investigated. In addition, the low-frequency noise and subthreshold swing degrade simultaneously in accordance to the device gate width scaling. Both serious subthreshold leakage and considerable noise can be attributed to the high trap density near the STI edge. Consequently, we propose a coincidental relationship between the noise level and the subthreshold characteristic; its trend is identical to the experiments and simulation results.

Increased risk of dental trauma in patients with allergic rhinitis: A nationwide population-based cohort study

Allergic rhinitis (AR) is associated with various developmental issues that affecting dentition. We aimed to determine whether AR is associated with an increased risk of traumatic dental injuries (TDIs) in Taiwanese individuals. We used the Taiwan National Health Insurance Research Database (NHIRD) to conduct a nested case-control study. We compared an AR cohort with a matched cohort of patients without AR. New TDI cases were determined during our study period. To compare TDI risk between our study cohorts, we used Cox proportional regression analysis, and hazard ratios (HR) with 95% confidence intervals (CI) were calculated to quantify the association between AR exposure and TDI risk. In total, 76749 patients with AR (31715 male; 45034 female) were identified. In the AR and the non-AR cohorts, 312 patients in total had TDI. Patients with AR had a significantly higher risk of TDI than those without AR (aHR = 1.92; 95% CI = 1.459-2.525; P < 0.001). The risk of TDI was markedly higher in the AR cohort, except in the 3-12-year-old group, and with a CCI ≥ 1. AR patients had a future risk of TDI, indicating a potentially linked disease pathophysiology. The association between AR and TDI is greater among general patients. Clinicians and caregivers should be aware of potential TDI co-morbidity in patients with AR.

Ankylosing spondylitis and the risk of cancer

Cancer is a multifactorial disease, and imbalances of the immune response and sex-associated features are considered risk factors for certain types of cancer. The present study aimed to assess whether ankylosing spondylitis (AS), an immune disorder that predominantly affects young adult men, is associated with an increased risk of cancer. Using the Taiwan National Health Insurance Research Database, a cohort of patients diagnosed with AS between 2000 and 2008 who had no history of cancer prior to enrollment was established (n=5,452). Age- and sex-matched patients without AS served as controls (n=21,808). The results revealed that the overall incidence of cancer was elevated in patients with AS [standardized incidence ratio (SIR), 1.15; 95% confidence interval (CI), 1.03-1.27]. AS carried an increased risk of hematological malignancy in both sexes, colon cancer in females and bone and prostate cancer in males. Young patients with AS (≤35 years) and patients with a Charlson comorbidity index (CCI) ≥2 experienced a higher incidence of cancer (males, SIR 1.92, and 95% CI 1.04-3.26; females, SIR 2.00 and 95% CI 1.46-5.50). The cancer risk was increased during the first 3 years following the diagnosis of AS (SIR 1.49, 95% CI 1.29-1.71), and overall cancer-free survival was significantly decreased in patients with AS patients of both sexes (P<0.0001). Therefore, AS was found to be associated with an increased risk of cancer. All AS patients must be screened for hematological malignancies, for prostate and bone cancer in males, and for colon cancer in females, particularly younger patients with a CCI ≥2.

Hepatoprotective effects of litchi (Litchi chinensis) procyanidin A2 on carbon tetrachloride-induced liver injury in ICR mice

Drug tolerance, lacking liver regenerative activity and inconclusive inhibition of steatosis and cirrhosis by silymarin treatment during chronic liver injury have increased the demand for novel alternative or synergistic treatments for liver damage. Litchi fruit is abundant in polyphenolic compounds and is used in traditional Chinese medicine for treatments that include the strengthening of hepatic and pancreatic functions. Unique polyphenolic compounds obtained from litchi pericarp extract (LPE) were studied in vitro and in vivo for hepatoprotection. Epicatechin (EC) and procyanidin A2 (PA2) of LPE were obtained by fractionated-extraction from pulverized litchi pericarps. All fractions, including LPE, were screened against silymarin in carbon tetrachloride (CCl₄)-treated murine embryonic liver cell line (BNL). The effects of daily gavage-feeding of LPE, silymarin (200 mg/kg body weight) or H₂O in CCl₄-intoxicated male ICR mice were evaluated by studying serum chemicals, liver pathology and glutathione antioxidative enzymes. The effects of EC and PA2 on liver cell regenerative activity were investigated using a scratch wound healing assay and flow cytometric cell cycle analysis; the results of which demonstrated that LPE protected BNL from CCl₄-intoxication. Gavage-feeding of LPE decreased serum glutamic oxaloacetate transaminase and glutamic pyruvic transaminase levels, and exhibited superior retention of the hexagonal structure of hepatocytes and reduced necrotic cells following liver histopathological examinations in CCl_4-intoxicated ICR mice. Glutathione peroxidise and glutathione reductase activities were preserved as the normal control level in LPE groups. EC and PA2 were principle components of LPE. PA2 demonstrated liver cell regenerative activity in scratch wound healing assays and alcohol-induced liver cell injury in vitro. The present findings suggest that litchi pericarp polyphenolic extracts, including EC and PA2, may be a synergistic alternative to silymarin in hepatoprotection and liver cell regeneration.

Miniature Surface Plasmon Polariton Amplitude Modulator by Beat Frequency and Polarization Control

The miniaturization of modulators keeps pace for the compact devices in optical applications. Here, we present a miniature surface plasmon polariton amplitude modulator (SPPAM) by directing and interfering surface plasmon polaritons on a nanofabricated chip. Our results show that this SPPAM enables two kinds of modulations. The first kind of modulation is controlled by encoding angular-frequency difference from a Zeeman laser, with a beat frequency of 1.66 MHz; the second of modulation is validated by periodically varying the polarization states from a polarization generator, with rotation frequencies of 0.5–10 k Hz. In addition, the normalized extinction ratio of our plasmonic structure reaches 100. Such miniaturized beat-frequency and polarization-controlled amplitude modulators open an avenue for the exploration of ultrasensitive nanosensors, nanocircuits, and other integrated nanophotonic devices.

Evaluation of nasal patency by visual analogue scale/nasal obstruction symptom evaluation questionnaires and anterior active rhinomanometry after septoplasty: a retrospective one-year follow-up cohort study

OBJECTIVE

To assess the efficacy of septoplasty and the correlation between the subjective evaluations of a visual analogue scale (VAS) and the Nasal Obstruction Symptom Evaluation (NOSE) questionnaire and active anterior rhinomanometry of the nasal airway after septoplasty.

DESIGN

A retrospective, individual cohort study.

SETTING

Ear, Nose and Throat Department, Taipei City Hospital, Taipei, Taiwan.

PARTICIPANTS

Fifty patients with chronic nasal obstruction were enrolled in the study. All 50 patients underwent septoplasty because of nasal septal deviation. Another 28 patients without nasal symptoms served as controls.

MAIN OUTCOME MEASURES

VAS, NOSE and active anterior rhinomanometry were used to measure the sensation of nasal obstruction. All measurements were performed in both groups preoperatively and then repeated on three postoperative visits (3, 6 and 12 months).

RESULTS

The mean VAS score, NOSE score and the nasal resistance in the narrow side of the nose in the study group showed reduced symptoms at 3, 6 and 12 months postoperatively compared with the respective preoperative measurements (P < 0.001, all). The VAS and NOSE scores did not significantly correlate with total nasal resistance preoperatively or postoperatively. The VAS and nasal resistance in the obstructed nasal cavity correlated significantly preoperatively (P < 0.05), but not postoperatively.

CONCLUSIONS

The subjective and objective symptoms of nasal obstruction had improved 1 year after septoplasty. A significant correlation between VAS scores and nasal resistance in the narrow side of the nose was found before surgery. The subjective and objective measurements of nasal obstruction lacked significant correlation postoperatively.

Mean Daily Dosage of Aspirin and the Risk of Incident Alzheimer's Dementia in Patients with Type 2 Diabetes Mellitus: A Nationwide Retrospective Cohort Study in Taiwan

Background. Type 2 diabetes mellitus patients are known to have higher risk of developing dementia while aspirin use has been shown to prevent incident dementia. This study was conducted to evaluate the potential benefits of aspirin use on dementia in patients with type 2 diabetes mellitus and identify the appropriate dosage of aspirin that provides the most benefit. Method. A Taiwan nationwide, population-based retrospective 8-year study was employed to analyze the association between the use of aspirin and incidence of dementia including Alzheimer's disease and non-Alzheimer's dementia using multivariate Cox-proportional hazards regression model and adjusting for several potential confounders. Results. Regular aspirin use in mean daily dosage of within 40 mg was associated with a decreased risk of developing incident Alzheimer's dementia in patients with type 2 diabetes mellitus (adjusted HR of 0.51 with 95% CI of 0.27-0.97, p value 0.041). Conclusion. A mean daily dosage of aspirin use within 40 mg might decrease the risk of developing Alzheimer's disease in patients with type 2 diabetes mellitus.

Risk of Tuberculosis in Children with Juvenile Idiopathic Arthritis: A Nationwide Population-Based Study in Taiwan

Objective

We aimed to determine the risk of tuberculosis in children with juvenile idiopathic arthritis (JIA) in Taiwan.

Methods

We used the Taiwan National Health Insurance Research Database (NHIRD) to conduct a nested case-control study. We identified a JIA cohort and matched each JIA child with non-JIA children for comparison. Methotrexate (MTX), tumor necrosis factor (TNF) inhibitor administration, and new tuberculosis cases were determined during our study period. To compare tuberculosis (TB) risk among our study groups, Cox proportional regression models were used to determine adjusted hazard ratios (aHRs).

Results

We identified 1495 children with JIA and 11592 non-JIA children. Majority (68.7%) children with JIA had not received MTX or TNF inhibitors; 23.9% used MTX without TNF inhibitors, and 7.4% received TNF inhibitors, irrespective of MTX administration. In total, 43 children developed tuberculosis. The overall tuberculosis infection rate for children with JIA was two times higher than that for non-JIA children. Compared with non-JIA children, children with JIA who used MTX without TNF inhibitors revealed a significantly increased of tuberculosis infection rate (aHR = 4.67; 95% CI: 1.65–13.17; P = 0.004). Children with JIA who either received TNF inhibitors or never used MTX and TNF inhibitors revealed a tuberculosis infection rate comparable to that of non-JIA children.

Conclusions

Analysis of nationwide data of Taiwan suggested that children with JIA were at higher risk of tuberculosis compared with those without JIA.

Designer germanium quantum dot phototransistor for near infrared optical detection and amplification

We demonstrated a unique CMOS approach for the production of a high-performance germanium (Ge) quantum dot (QD) metal-oxide-semiconductor phototransistor. In the darkness, low off-state leakage (Ioff ∼ 0.27 pA μm(-2)), a high on-off current ratio (Ion/Ioff ∼ 10(6)), and good switching behaviors (subthreshold swing of 175 mV/dec) were measured on our Ge-QD phototransistor at 300 K, indicating good hetero-interfacial quality of the Ge-on-Si. Illumination makes a significant enhancement in the drain current of Ge QD phototransistors when biased at both the on- and off-states, which is a great benefit from Ge QD-mediated photoconductive and photovoltaic effects. The measured photocurrent-to-dark-current ratio (Iphoto/Idark) and the photoresponsivities from the Ge QD phototransistor are as high as 4.1 × 10(6) and 1.7 A W(-1), respectively, under an incident power of 0.9 mW at 850 nm illumination. A superior external quantum efficiency of 240% and a very fast temporal response time of 1.4 ns suggest that our Ge QD MOS phototransistor offers great promise as optical switches and transducers for Si-based optical interconnects.

Distinct epidermal keratinocytes respond to extremely low-frequency electromagnetic fields differently

Following an increase in the use of electric appliances that can generate 50 or 60 Hz electromagnetic fields, concerns have intensified regarding the biological effects of extremely low-frequency electromagnetic fields (ELF-EMFs) on human health. Previous epidemiological studies have suggested the carcinogenic potential of environmental exposure to ELF-EMFs, specifically at 50 or 60 Hz. However, the biological mechanism facilitating the effects of ELF-EMFs remains unclear. Cellular studies have yielded inconsistent results regarding the biological effects of ELF-EMFs. The inconsistent results might have been due to diverse cell types. In our previous study, we indicated that 1.5 mT, 60 Hz ELF-EMFs will cause G1 arrest through the activation of the ATM-Chk2-p21 pathway in human keratinocyte HaCaT cells. The aim of the current study was to investigate whether ELF-EMFs cause similar effects in a distinct epidermal keratinocyte, primary normal human epidermal keratinocytes (NHEK), by using the same ELF-EMF exposure system and experimental design. We observed that ELF-EMFs exerted no effects on cell growth, cell proliferation, cell cycle distribution, and the activation of ATM signaling pathway in NHEK cells. We demonstrated that the 2 epidermal keratinocytes responded to ELF-EMFs differently. To further validate this finding, we simultaneously exposed the NHEK and HaCaT cells to ELF-EMFs in the same incubator for 168 h and observed the cell growths. The simultaneous exposure of the two cell types results showed that the NHEK and HaCaT cells exhibited distinct responses to ELF-EMFs. Thus, we confirmed that the biological effects of ELF-EMFs in epidermal keratinocytes are cell type specific. Our findings may partially explain the inconsistent results of previous studies when comparing results across various experimental models.

Identification of under-detected periodicity in time-series microarray data by using empirical mode decomposition

Detecting periodicity signals from time-series microarray data is commonly used to facilitate the understanding of the critical roles and underlying mechanisms of regulatory transcriptomes. However, time-series microarray data are noisy. How the temporal data structure affects the performance of periodicity detection has remained elusive. We present a novel method based on empirical mode decomposition (EMD) to examine this effect. We applied EMD to a yeast microarray dataset and extracted a series of intrinsic mode function (IMF) oscillations from the time-series data. Our analysis indicated that many periodically expressed genes might have been under-detected in the original analysis because of interference between decomposed IMF oscillations. By validating a protein complex coexpression analysis, we revealed that 56 genes were newly determined as periodic. We demonstrated that EMD can be used incorporating with existing periodicity detection methods to improve their performance. This approach can be applied to other time-series microarray studies.

Transcriptome profiling in imipenem-selected Acinetobacter baumannii

BACKGROUND

Carbapenem-resistance in Acinetobacter baumannii has gradually become a global challenge. To identify the genes involved in carbapenem resistance in A. baumannii, the transcriptomic responses of the completely sequenced strain ATCC 17978 selected with 0.5 mg/L (IPM-2 m) and 2 mg/L (IPM-8 m) imipenem were investigated using RNA-sequencing to identify differences in the gene expression patterns.

RESULTS

A total of 88 and 68 genes were differentially expressed in response to IPM-2 m and IPM-8 m selection, respectively. Among the expressed genes, 50 genes were highly expressed in IPM-2 m, 30 genes were highly expressed in IPM-8 m, and 38 genes were expressed common in both strains. Six groups of genes were simultaneously expressed in IPM-2 m and IPM-8 m mutants. The three gene groups involved in DNA recombination were up-regulated, including recombinase, transposase and DNA repair, and beta-lactamase OXA-95 and homologous recombination. The remaining gene groups involved in biofilm formation were down-regulated, including quorum sensing, secretion systems, and the csu operon. The antibiotic resistance determinants, including RND efflux transporters and multidrug resistance pumps, were over-expressed in response to IPM-2 m selection, followed by a decrease in response to IPM-8 m selection. Among the genes over-expressed in both strains, blaOXA-95, previously clustered with the blaOXA-51-like family, showed 14-fold (IPM-2 m) to 330-fold (IPM-8 m) over-expression. The expression of blaOXA-95 in IPM-2 m and IPM-8 m cells was positively correlated with the rate of imipenem hydrolysis, as demonstrated through Liquid Chromatography-Mass Spectrometry/Mass Spectrometry, suggesting that blaOXA-95 plays a critical role in conferring carbapenem resistance. In addition, A. baumannii shows an inverse relationship between carbapenem resistance and biofilm production.

CONCLUSION

Gene recombination and blaOXA-95 play critical roles in carbapenem resistance in A. baumannii. Taken together, the results of the present study provide a foundation for future studies of the network systems associated with carbapenem resistance.

Population-based cohort study on the risk of malignancy in East Asian children with juvenile idiopathic arthritis

BACKGROUND

To investigate the association and magnitude of risk between JIA, its associated treatment and cancer development in Taiwanese children.

METHODS

Nationwide population-based 1:4 age- and gender-matched retrospective cohort study was designed using the National Health Insurance Research Database of Taiwan. A cohort of 2,892 children <16 years old with JIA was formed as well as a non-JIA cohort of 11,568 in year 2003 to 2005. They were followed up till a diagnosis of malignancy or up to 8 years until 2010. Relative risk (RR), incidence rate ratio (IRR), and adjusted hazard ratio (aHR) of developing malignancy were calculated.

RESULTS

The female to male ratio was 0.79:1. There were 3 cases of incident cancer in the "MTX use, biologics-naïve" group, only 1 in the anti-TNF biologics-containing group and 29 in the "both MTX- and biologics-naïve" group, in comparison, there were 50 cases of cancer in the non-JIA comparator group. During a 16114.16 patient-years follow-up, the RR and IRR for developing a malignancy in both methotrexate- and anti-tumor necrosis factor (TNF) biologics-naïve JIA children were 2.75 (95% confidence interval, 1.75 - 4.32) and 3.21 (2.01 - 5.05), respectively. For leukemia, the IRR was 7.38 (2.50 - 22.75); lymphoma, 8.30 (1.23 - 69.79); and soft tissue sarcoma, 11.07 (0.84 - 326.4). The IRR of other cancers was 2.08 (1.11 - 3.71). The aHR on cancer risk was 3.14 (1.98 - 4.98) in methotrexate- and biologics-naïve group. There were no statistically significant increased risk in JIA patients treated with methotrexate and/or anti-TNF biologics.

CONCLUSIONS

Compared with children without JIA, children with JIA have 3-fold increase of risk on malignancy in East Asia. Seemingly neither methotrexate nor anti-TNF biologics increases the risk further.

Extremely low-frequency electromagnetic fields cause G1 phase arrest through the activation of the ATM-Chk2-p21 pathway

In daily life, humans are exposed to the extremely low-frequency electromagnetic fields (ELF-EMFs) generated by electric appliances, and public concern is increasing regarding the biological effects of such exposure. Numerous studies have yielded inconsistent results regarding the biological effects of ELF-EMF exposure. Here we show that ELF-EMFs activate the ATM-Chk2-p21 pathway in HaCaT cells, inhibiting cell proliferation. To present well-founded results, we comprehensively evaluated the biological effects of ELF-EMFs at the transcriptional, protein, and cellular levels. Human HaCaT cells from an immortalized epidermal keratinocyte cell line were exposed to a 1.5 mT, 60 Hz ELF-EMF for 144 h. The ELF-EMF could cause G1 arrest and decrease colony formation. Protein expression experiments revealed that ELF-EMFs induced the activation of the ATM/Chk2 signaling cascades. In addition, the p21 protein, a regulator of cell cycle progression at G1 and G2/M, exhibited a higher level of expression in exposed HaCaT cells compared with the expression of sham-exposed cells. The ELF-EMF-induced G1 arrest was diminished when the CHK2 gene expression (which encodes checkpoint kinase 2; Chk2) was suppressed by specific small interfering RNA (siRNA). These findings indicate that ELF-EMFs activate the ATM-Chk2-p21 pathway in HaCaT cells, resulting in cell cycle arrest at the G1 phase. Based on the precise control of the ELF-EMF exposure and rigorous sham-exposure experiments, all transcriptional, protein, and cellular level experiments consistently supported the conclusion. This is the first study to confirm that a specific pathway is triggered by ELF-EMF exposure.

HNO₃-assisted polyol synthesis of ultralarge single-crystalline Ag microplates and their far propagation length of surface plasmon polariton

We developed a HNO3-assisted polyol reduction method to synthesize ultralarge single-crystalline Ag microplates routinely. The edge length of the synthesized Ag microplates reaches 50 μm, and their top facets are (111). The mechanism for dramatically enlarging single-crystalline Ag structure stems from a series of competitive anisotropic growths, primarily governed by carefully tuning the adsorption of Ag(0) by ethylene glycol and the desorption of Ag(0) by a cyanide ion on Ag(100). Finally, we measured the propagation length of surface plasmon polaritons along the air/Ag interface under 534 nm laser excitation. Our single-crystalline Ag microplate exhibited a propagation length (11.22 μm) considerably greater than that of the conventional E-gun deposited Ag thin film (5.27 μm).

Effects of statins on incident dementia in patients with type 2 DM: a population-based retrospective cohort study in Taiwan

BACKGROUND

Patients with Type 2 diabetes (T2DM) are prone to develop dementia. Results from a recent study indicated that statin users had lower chance of developing incident dementia. However there is little information on the potential benefits of statin use on dementia in patients with T2DM cohort.

METHOD

A population-based retrospective study using a nationwide cohort of National Health Insurance Research Database in Taiwan was performed. T2DM cohort with regular use of statins was followed up to 8 years. Multivariate cox-proportional hazards regression model was used to estimate the association between statin use and incidence of dementia including Alzheimer's disease and non-Alzheimer dementia after adjusting for several potential confounders.

RESULTS

Among 28,321 patients diagnosed with T2DM age above 50 and without history of dementia before 2000/1/1, 15,770 patients who had never used statin and 2,400 patients who regularly used statin drugs were enrolled. After adjusting for age group, gender, CCI (Charlson-Deyo comorbidity index) group, stroke types and anti-diabetic drugs, regular statin use was associated with a decreased risk of developing incident Alzheimer's disease dementia (adjusted HR: 0.48, 95% CI 0.30 - 0.76, p<0.001), but not in non-Alzheimer dementia (adjusted HR: 1.07, 95% CI 0.54-2.12 p = 0.844) in patients with T2DM. Further analysis showed significant protective effects of the use of atorvastatin and simvastatin.

CONCLUSION

Regular use of statins might decrease the risk of developing Alzheimer's disease in patients with T2DM while no benefit was observed in non-Alzheimer dementia. Among statins, both atorvastatin and simvastatin showed significant benefits.

Identification and characterization of lysine-methylated sites on histones and non-histone proteins

Protein methylation is a kind of post-translational modification (PTM), and typically takes place on lysine and arginine amino acid residues. Protein methylation is involved in many important biological processes, and most recent studies focused on lysine methylation of histones due to its critical roles in regulating transcriptional repression and activation. Histones possess highly conserved sequences and are homologous in most species. However, there is much less sequence conservation among non-histone proteins. Therefore, mechanisms for identifying lysine-methylated sites may greatly differ between histones and non-histone proteins. Nevertheless, this point of view was not considered in previous studies. Here we constructed two support vector machine (SVM) models by using lysine-methylated data from histones and non-histone proteins for predictions of lysine-methylated sites. Numerous features, such as the amino acid composition (AAC) and accessible surface area (ASA), were used in the SVM models, and the predictive performance was evaluated using five-fold cross-validations. For histones, the predictive sensitivity was 85.62% and specificity was 80.32%. For non-histone proteins, the predictive sensitivity was 69.1% and specificity was 88.72%. Results showed that our model significantly improved the predictive accuracy of histones compared to previous approaches. In addition, features of the flanking region of lysine-methylated sites on histones and non-histone proteins were also characterized and are discussed. A gene ontology functional analysis of lysine-methylated proteins and correlations of lysine-methylated sites with other PTMs in histones were also analyzed in detail. Finally, a web server, MethyK, was constructed to identify lysine-methylated sites. MethK now is available at http://csb.cse.yzu.edu.tw/MethK/.

A novel approach for discovering condition-specific correlations of gene expressions within biological pathways by using cloud computing technology

Microarrays are widely used to assess gene expressions. Most microarray studies focus primarily on identifying differential gene expressions between conditions (e.g., cancer versus normal cells), for discovering the major factors that cause diseases. Because previous studies have not identified the correlations of differential gene expression between conditions, crucial but abnormal regulations that cause diseases might have been disregarded. This paper proposes an approach for discovering the condition-specific correlations of gene expressions within biological pathways. Because analyzing gene expression correlations is time consuming, an Apache Hadoop cloud computing platform was implemented. Three microarray data sets of breast cancer were collected from the Gene Expression Omnibus, and pathway information from the Kyoto Encyclopedia of Genes and Genomes was applied for discovering meaningful biological correlations. The results showed that adopting the Hadoop platform considerably decreased the computation time. Several correlations of differential gene expressions were discovered between the relapse and nonrelapse breast cancer samples, and most of them were involved in cancer regulation and cancer-related pathways. The results showed that breast cancer recurrence might be highly associated with the abnormal regulations of these gene pairs, rather than with their individual expression levels. The proposed method was computationally efficient and reliable, and stable results were obtained when different data sets were used. The proposed method is effective in identifying meaningful biological regulation patterns between conditions.

Acarbose treatment and the risk of cardiovascular disease in type 2 diabetic patients: a nationwide seven-year follow-up study

OBJECTIVE

To investigate the potential benefits of acarbose treatment on cardiovascular disease (CVD) in patients with type 2 diabetes by using nationwide insurance claim dataset.

RESEARCH DESIGN AND METHODS

Among 644,792 newly diagnosed type 2 diabetic patients without preexisting CVD in a nationwide cohort study, 109,139 (16.9%) who had received acarbose treatment were analyzed for CVD risk. Those with CVD followed by acarbose therapy were also subjected to analysis.

RESULT

During 7 years of follow-up, 5,081 patients (4.7%) developed CVD. The crude hazard ratio (HR) and adjusted HR were 0.66 and 0.99, respectively. The adjusted HR of CVD was 1.19, 0.70, and 0.38 when the duration of acarbose use was <12 months, 12-24 months, and >24 months, respectively. Adjusted HR was 1.14, 0.64, and 0.41 with acarbose cumulative doses <54,750 mg, 54,751 to 109,500 mg, and >109,500 mg, respectively.

CONCLUSION

In patients with type 2 diabetes without preexisting CVD, treatment with acarbose showed a transient increase in incidence of CVD in the initial 12 months followed by significant reductions of CVD in prolonged acarbose users. After the first CVD events, continuous use of acarbose revealed neutral effect within the first 12 months. The underlying mechanisms require further investigations.

Serine protease inhibitor gabexate mesilate attenuates american cockroach-induced bronchial damage and inflammatory cytokine release

BACKGROUND AND OBJECTIVE

Allergic airway diseases are not only a T,2-mediated chronic airway inflammation, but also a condition of epithelial barrier defects and dysfunction. Allergens with protease activities are known factors that initiate respiratory epithelial damage. Cockroach allergy is the second leading cause of allergic respiratory airway diseases in Taiwan, and cockroach allergens have strong serine protease activity. This study aimed to determine the protective effect of the direct local administration of gabexate mesilate (GM) on American cockroach allergen (CraA)-induced human bronchial epithelial cell inflammation.

METHODS

BEAS-2B cells, from the human bronchial epithelial cell line, were stimulated with CraA or co-cultured with different doses of GM. Cellular morphologic changes were observed by microscopy and changes in chemokine mRNA expression and protein levels were determined by semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) and ELISA. Effects of specific inhibitors of ERK1/2 (U0126), INK (SP600125), and p38 MAPK (SB203580) on CraA-induced chemokine mRNA expression were also tested by RT-PCR.

RESULTS

GM prevented CraA-induced bronchial epithelial cell detachment and morphological changes. It had superior and more extensive suppression effects than specific target MAPK inhibitors in CraA-induced mRNA expression of IL-8, monocyte chemotactic protein (MCP) 1, chemokine (C-C motif) ligand 20, and granulocyte-macrophage colony-stimulating factor from the cells in a dose-dependent manner. CraA-induced IL-8 and MCP-1 protein production from BEAS-2B cells was also attenuated by GM.

CONCLUSIONS

The serine protease inhibitor GM has local protective effects against CraA-induced bronchial epithelial inflammation. The development of an inhaled or intranasal protease inhibitor may be a potential strategy for the treatment of allergic airway diseases induced by allergens with protease activities.

Evaluation of the appropriate age range of colorectal cancer screening based on the changing epidemiology in the past 20 years in taiwan

Introduction. According to the recommendation of the United States Preventative Services Task Force, most countries provide average-risk screening for colorectal cancers (CRCs) between the ages of 50 and 75 years. However, the age range of screening should be modified because of an increasing life span. Methods. Totally 124,314 CRC cases were registered in Taiwan Cancer Registry from 1988 to 2007. The 20-year study period was divided into four 5-year increments. We divided the patients into four age groups (under age 50, age 50–74, age 74–84, and over age 85) in each increment to determine whether there were changes in the age distribution. Results. In the subgroup of patients under age 50, the number of CRC cases increased, but they accounted for a decreasing proportion of the total CRCs. In the 50–74 age group, the proportion of CRC cases also dropped. In contrast, the proportion increased in the 75–84 age group. Therefore, 43.63% of CRC patients would not be delegated to screen in the period of 2003–2007 if the CRC screening were restricted in the 50–74 age group. Conclusions. CRC screening for healthy individuals aged over 75 years is necessary.

Gene expression profiling of dendritic cells in different physiological stages under Cordyceps sinensis treatment

Cordyceps sinensis (CS) has been commonly used as herbal medicine and a health supplement in China for over two thousand years. Although previous studies have demonstrated that CS has benefits in immunoregulation and anti-inflammation, the precise mechanism by which CS affects immunomodulation is still unclear. In this study, we exploited duplicate sets of loop-design microarray experiments to examine two different batches of CS and analyze the effects of CS on dendritic cells (DCs), in different physiology stages: naïve stage and inflammatory stage. Immature DCs were treated with CS, lipopolysaccharide (LPS), or LPS plus CS (LPS/CS) for two days, and the gene expression profiles were examined using cDNA microarrays. The results of two loop-design microarray experiments showed good intersection rates. The expression level of common genes found in both loop-design microarray experiments was consistent, and the correlation coefficients (Rs), were higher than 0.96. Through intersection analysis of microarray results, we identified 295 intersecting significantly differentially expressed (SDE) genes of the three different treatments (CS, LPS, and LPS/CS), which participated mainly in the adjustment of immune response and the regulation of cell proliferation and death. Genes regulated uniquely by CS treatment were significantly involved in the regulation of focal adhesion pathway, ECM-receptor interaction pathway, and hematopoietic cell lineage pathway. Unique LPS regulated genes were significantly involved in the regulation of Toll-like receptor signaling pathway, systemic lupus erythematosus pathway, and complement and coagulation cascades pathway. Unique LPS/CS regulated genes were significantly involved in the regulation of oxidative phosphorylation pathway. These results could provide useful information in further study of the pharmacological mechanisms of CS. This study also demonstrates that with a rigorous experimental design, the biological effects of a complex compound can be reliably studied by a complex system like cDNA microarray.

Diabetic patients with severe sepsis admitted to intensive care unit do not fare worse than non-diabetic patients: a nationwide population-based cohort study

BACKGROUND

We sought to examine whether type 2 diabetes increases the risk of acute organ dysfunction and of hospital mortality following severe sepsis that requires admission to an intensive care unit (ICU).

METHODS

Nationwide population-based retrospective cohort study of 16,497 subjects with severe sepsis who had been admitted for the first time to an ICU during the period of 1998-2008. A diabetic cohort (n = 4573) and a non-diabetic cohort (n = 11924) were then created. Relative risk (RR) of organ dysfunctions, length of hospital stay (LOS), 90-days hospital mortality, ICU resource utilization and hazard ratio (HR) of mortality adjusted for age, gender, Charlson-Deyo comorbidity index score, surgical condition and number of acute organ dysfunction, were compared across patients with severe sepsis with or without diabetes.

RESULTS

Diabetic patients with sepsis had a higher risk of developing acute kidney injury (RR, 1.54; 95% confidence interval (CI), 1.44-1.63) and were more likely to be undergoing hemodialysis (15.55% vs. 7.24%) in the ICU. However, the diabetic cohort had a lower risk of developing acute respiratory dysfunction (RR = 0.96, 0.94-0.97), hematological dysfunction (RR = 0.70, 0.56-0.89), and hepatic dysfunction (RR = 0.77, 0.63-0.93). In terms of adjusted HR for 90-days hospital mortality, the diabetic patients with severe sepsis did not fare significantly worse when afflicted with cardiovascular, respiratory, hepatic, renal and/or neurologic organ dysfunction and by numbers of organ dysfunction. There was no statistically significant difference in LOS between the two cohorts (median 17 vs. 16 days, interquartile range (IQR) 8-30 days, p = 0.11). Multiple logistic regression analysis to predict the occurrence of mortality shows that being diabetic was not a predictive factor with an odds ratio of 0.972, 95% CI 0.890-1.061, p = 0.5203.

INTERPRETATION

This large nationwide population-based cohort study suggests that diabetic patients do not fare worse than non-diabetic patients when suffering from severe sepsis that requires ICU admission.

Repeated small perturbation approach reveals transcriptomic steady states

The study of biological systems dynamics requires elucidation of the transitions of steady states. A "small perturbation" approach can provide important information on the "steady state" of a biological system. In our experiments, small perturbations were generated by applying a series of repeating small doses of ultraviolet radiation to a human keratinocyte cell line, HaCaT. The biological response was assessed by monitoring the gene expression profiles using cDNA microarrays. Repeated small doses (10 J/m2) of ultraviolet B (UVB) exposure modulated the expression profiles of two groups of genes in opposite directions. The genes that were up-regulated have functions mainly associated with anti-proliferation/anti-mitogenesis/apoptosis, and the genes that were down-regulated were mainly related to proliferation/mitogenesis/anti-apoptosis. For both groups of genes, repetition of the small doses of UVB caused an immediate response followed by relaxation between successive small perturbations. This cyclic pattern was suppressed when large doses (233 or 582.5 J/m2) of UVB were applied. Our method and results contribute to a foundation for computational systems biology, which implicitly uses the concept of steady state.

Smart sensor systems for human health breath monitoring applications

Breath analysis techniques offer a potential revolution in health care diagnostics, especially if these techniques can be brought into standard use in the clinic and at home. The advent of microsensors combined with smart sensor system technology enables a new generation of sensor systems with significantly enhanced capabilities and minimal size, weight and power consumption. This paper discusses the microsensor/smart sensor system approach and provides a summary of efforts to migrate this technology into human health breath monitoring applications. First, the basic capability of this approach to measure exhaled breath associated with exercise physiology is demonstrated. Building from this foundation, the development of a system for a portable asthma home health care system is described. A solid-state nitric oxide (NO) sensor for asthma monitoring has been identified, and efforts are underway to miniaturize this NO sensor technology and integrate it into a smart sensor system. It is concluded that base platform microsensor technology combined with smart sensor systems can address the needs of a range of breath monitoring applications and enable new capabilities for healthcare.

Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis

Background

Categorizing protein-encoding transcriptomes of normal tissues into housekeeping genes and tissue-selective genes is a fundamental step toward studies of genetic functions and genetic associations to tissue-specific diseases. Previous studies have been mainly based on a few data sets with limited samples in each tissue, which restrained the representativeness of their identified genes, and resulted in low consensus among them.

Results

This study compiled 1,431 samples in 43 normal human tissues from 104 microarray data sets. We developed a new method to improve gene expression assessment, and showed that more than ten samples are needed to robustly identify the protein-encoding transcriptome of a tissue. We identified 2,064 housekeeping genes and 2,293 tissue-selective genes, and analyzed gene lists by functional enrichment analysis. The housekeeping genes are mainly involved in fundamental cellular functions, and the tissue-selective genes are strikingly related to functions and diseases corresponding to tissue-origin. We also compared agreements and related functions among our housekeeping genes and those of previous studies, and pointed out some reasons for the low consensuses.

Conclusions

The results indicate that sufficient samples have improved the identification of protein-encoding transcriptome of a tissue. Comprehensive meta-analysis has proved the high quality of our identified HK and TS genes. These results could offer a useful resource for future research on functional and genomic features of HK and TS genes.

Effect of dopants on the soft magnetic properties and high frequency characteristics of FeCoBM (M = Ti, Nb, Hf, and Ta) thin films

Effect of dopants on the soft magnetic properties and high frequency characteristics of FeCoBM thin films (M = Ti, Nb, Hf, and Ta) have been studied. For (Fe0.55Co0.45)(100-x)B(x) (x = 5-15) thin films, with the increase of B content, the resistivity was increased because B could decrease the crystallinity of the films. The (Fe0.55Co0.45)90B10 thin film showed the optimum properties, where 4piM(s) = 16.1 kG, H(ce) = 64.2 Oe, H(ch) = 13.5 Oe, H(k) = 310 Oe and p = 338 microomega-cm. To reduce the coercivity of the film, the elements M, including Ti, Nb, Hf, and Ta, were selected to substitute for B in the FeCoB films. It was found that (Fe0.55Co0.45)90B6Ti2Nb2 thin film after annealing at a temperature of 200 degrees C for 30 min showed the optimal properties, where 4piM(s) = 15.8 kG, H(ce) = 4.8 Oe, H(ch) = 3.6 Oe, H(k) = 224 Oe and p = 290 microomega-cm. The theoretically calculated ferromagnetic resonance frequency of the developed films can be higher than 5 GHz.

Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis

Background

The accuracy of quantitative real-time PCR (qRT-PCR) is highly dependent on reliable reference gene(s). Some housekeeping genes which are commonly used for normalization are widely recognized as inappropriate in many experimental conditions. This study aimed to identify reference genes for clinical studies through microarray meta-analysis of human clinical samples.

Methodology/Principal Findings

After uniform data preprocessing and data quality control, 4,804 Affymetrix HU-133A arrays performed by clinical samples were classified into four physiological states with 13 organ/tissue types. We identified a list of reference genes for each organ/tissue types which exhibited stable expression across physiological states. Furthermore, 102 genes identified as reference gene candidates in multiple organ/tissue types were selected for further analysis. These genes have been frequently identified as housekeeping genes in previous studies, and approximately 71% of them fall into Gene Expression (GO:0010467) category in Gene Ontology.

Conclusions/Significance

Based on microarray meta-analysis of human clinical sample arrays, we identified sets of reference gene candidates for various organ/tissue types and then examined the functions of these genes. Additionally, we found that many of the reference genes are functionally related to transcription, RNA processing and translation. According to our results, researchers could select single or multiple reference gene(s) for normalization of qRT-PCR in clinical studies.

Green fabrication of agar-conjugated Fe3O4 magnetic nanoparticles

Magnetic nanoparticles are of great interest both for fundamental research and emerging applications. In the biomedical field, magnetite (Fe(3)O(4)) has shown promise as a hyperthermia-based tumor therapeutic. However, preparing suitable solubilized magnetite nanoparticles is challenging, primarily due to aggregation and poor biocompatibility. Thus methods for coating Fe(3)O(4) NPs with biocompatible stabilizers are required. We report a new method for preparing Fe(3)O(4) nanoparticles by co-precipitation within the pores of agar gel samples. Permeated agar gels were then dried and ground into a powder, yielding agar-conjugated Fe(3)O(4) nanoparticles. Samples were characterized using XRD, FTIR, TGA, TEM and SQUID. This method for preparing agar-coated Fe(3)O(4) nanoparticles is environmentally friendly, inexpensive and scalable.

Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database

Background

Over the past decade, gene expression microarray studies have greatly expanded our knowledge of genetic mechanisms of human diseases. Meta-analysis of substantial amounts of accumulated data, by integrating valuable information from multiple studies, is becoming more important in microarray research. However, collecting data of special interest from public microarray repositories often present major practical problems. Moreover, including low-quality data may significantly reduce meta-analysis efficiency.

Results

M²DB is a human curated microarray database designed for easy querying, based on clinical information and for interactive retrieval of either raw or uniformly pre-processed data, along with a set of quality-control metrics. The database contains more than 10,000 previously published Affymetrix GeneChip arrays, performed using human clinical specimens. M²DB allows online querying according to a flexible combination of five clinical annotations describing disease state and sampling location. These annotations were manually curated by controlled vocabularies, based on information obtained from GEO, ArrayExpress, and published papers. For array-based assessment control, the online query provides sets of QC metrics, generated using three available QC algorithms. Arrays with poor data quality can easily be excluded from the query interface. The query provides values from two algorithms for gene-based filtering, and raw data and three kinds of pre-processed data for downloading.

Conclusion

M²DB utilizes a user-friendly interface for QC parameters, sample clinical annotations, and data formats to help users obtain clinical metadata. This database provides a lower entry threshold and an integrated process of meta-analysis. We hope that this research will promote further evolution of microarray meta-analysis.

Subcutaneous administration of TC007 reduces disease severity in an animal model of SMA

Background

Spinal Muscular Atrophy (SMA) is the leading genetic cause of infantile death. It is caused by the loss of functional Survival Motor Neuron 1 (SMN1). There is a nearly identical copy gene, SMN2, but it is unable to rescue from disease due to an alternative splicing event that excises a necessary exon (exon 7) from the majority of SMN2-derived transcripts. While SMNΔ7 protein has severely reduced functionality, the exon 7 sequences may not be specifically required for all activities. Therefore, aminoglycoside antibiotics previously shown to suppress stop codon recognition and promote translation read-through have been examined to increase the length of the SMNΔ7 C-terminus.

Results

Here we demonstrate that subcutaneous-administration of a read-through inducing compound (TC007) to an intermediate SMA model (Smn-/-; SMN2+/+; SMNΔ7) had beneficial effects on muscle fiber size and gross motor function.

Conclusion

Delivery of the read-through inducing compound TC007 reduces the disease-associated phenotype in SMA mice, however, does not significantly extend survival.

Delivery of a read-through inducing compound, TC007, lessens the severity of a spinal muscular atrophy animal model

Spinal muscular atrophy (SMA) is the leading genetic cause of infant mortality and is caused by the loss of a functional SMN1 gene. In humans, there exists a nearly-identical copy gene known as SMN2 that encodes an identical protein as SMN1, but differs by a silent C to T transition within exon 7. This single nucleotide difference produces an alternatively spliced isoform, SMNDelta7, which encodes a rapidly degraded protein. The absence of the short peptide encoded by SMN exon 7 is critical in the disease development process; however, heterologous sequences can partially compensate for the SMN exon 7 peptide in several cellular assays. Consistent with this, aminoglycosides, compounds that can suppress efficient recognition of stop codons, resulted in significantly increased levels of SMN protein in SMA patient fibroblasts. We now examine the potential therapeutic capabilities of a novel aminoglycoside, TC007. In an intermediate SMA model (Smn-/-; SMN2+/+; SMNDelta7), when delivered directly to the central nervous system (CNS), TC007 induces SMN in both the brain and spinal cord, significantly increases lifespan ( approximately 30%) and increases ventral horn cell number, consistent with its ability to increase SMN levels in induced pluripotent stem cell-derived human SMA motor neuron cultures. Collectively, these experiments are the first in vivo examination of therapeutics for SMA designed to induce read-through of the SMNDelta7 stop codon to show increased benefit by direct administration to the CNS.

The robotic radiosynthesis of 5-[(18)F]fluoro-2'-deoxyuridine and its biological characterization

5-[(18)F]fluoro-2'-deoxyuridine ([(18)F]FUdR) was synthesized using a robotic system as a proliferation probe for PET. [(18)F]FUdR was prepared via radiofluorodestannylation reaction from its organotin precursor. Biodistribution study and microPET imaging of [(18)F]FUdR in NG4TL4 sarcoma-bearing FVB/n mice were performed. The tumor-to-blood and tumor-to-muscle ratio increased steadily from 15 (1.81 and 3.42) to 120min (9.10 and 11.9) post injection. The dynamic microPET imaging demonstrates remarkable radioactivity retention in the tumor, which is consistent with the results of biodistribution study.

Breakdown of Fourier's law in nanotube thermal conductors

We present experimental evidence that the room temperature thermal conductivity (kappa) of individual multiwalled carbon and boron-nitride nanotubes does not obey Fourier's empirical law of thermal conduction. Because of isotopic disorder, kappa's of carbon nanotubes and boron-nitride nanotubes show different length dependence behavior. Moreover, for these systems we find that Fourier's law is violated even when the phonon mean free path is much shorter than the sample length.

Statistical comparison of residential soil concentrations of PCDDs, PCDFs, and PCBs from two communities in Michigan

The University of Michigan dioxin exposure study was undertaken to address concerns that the industrial discharge of dioxin-like compounds in the Midland, MI area had resulted in contamination of soils in the Tittabawassee River floodplain and downwind of the incinerator. The study was designed in a rigorously statistical manner comprising soil measurements of 29 polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and polychlorinated biphenyls (PCBs) from 766 residential properties, selected probabilistically, in the Midland area and in Jackson and Calhoun Counties (Michigan) as a background comparison. A statistical comparison determined that the geometric mean toxic equivalent (TEQ) levels in samples from the target populations were statistically significantly above background. In addition, the probabilities of being above the 75th and 95th percentiles of background were also greater. Congener contributions to the TEQ were dominated by 2,3,4,7,8-PeCDF and 2,3,7,8-TCDF in the floodplain and by 2,3,7,8-TCDD in the incinerator plume. However, PCB 126 was the top congener contributing to the background TEQ. On the basis of statistical inference to the total population, it was estimated that about 36% of the properties in the floodplain and incinerator plume have at least one soil sample over the Michigan Department of Environmental Quality's soil direct contact criterion of 90 pg/g TEQ.

Medial antebrachial cutaneous neuropathy: a case report

Medial antebrachial cutaneous (MABC) neuropathy in the forearm is rare. We report here a case of this neuropathy after surgery for panniculitis excision. Examination revealed hypesthesia over left medial forearm at MABC nerve territory. Tineal's sign at the operation site of left medial arm was positive. Sensory nerve conduction studies showed reduced sensory nerve action potential amplitude which is compatible with an axonal neuropathy and interside amplitude ratio of 2.35. In the present case report, the sensory nerve conduction study is a useful tool in confirming MABC neuropathy.