PRoNTo: pattern recognition for neuroimaging toolbox

In the past years, mass univariate statistical analyses of neuroimaging data have been complemented by the use of multivariate pattern analyses, especially based on machine learning models. While these allow an increased sensitivity for the detection of spatially distributed effects compared to univariate techniques, they lack an established and accessible software framework. The goal of this work was to build a toolbox comprising all the necessary functionalities for multivariate analyses of neuroimaging data, based on machine learning models. The “Pattern Recognition for Neuroimaging Toolbox” (PRoNTo) is open-source, cross-platform, MATLAB-based and SPM compatible, therefore being suitable for both cognitive and clinical neuroscience research. In addition, it is designed to facilitate novel contributions from developers, aiming to improve the interaction between the neuroimaging and machine learning communities. Here, we introduce PRoNTo by presenting examples of possible research questions that can be addressed with the machine learning framework implemented in PRoNTo, and cannot be easily investigated with mass univariate statistical analysis.

Body mass index and risk of pneumonia: a systematic review and meta-analysis

The aims of our meta-analysis were to examine the pattern and gender's influence on body mass index (BMI) - pneumonia relationship. Published studies were searched from PubMed, Web of Science, Cochrane Library databases using keywords of pneumonia, BMI and epidemiologic studies. Random-effects analysis was applied to estimate pooled effect sizes from individual studies. The Cochrane Q-test and index of heterogeneity (I(2) ) were used to evaluate heterogeneity, and Egger's test was used to evaluate publication bias. Random-effects meta-regression was applied to examine the pattern and gender's influence on BMI-pneumonia relationship. A total of 1,531 studies were initially identified, and 25 studies finally were included. The pooled relative risk (RR) and meta-regression model revealed a J-shaped relationship between BMI and risk of community-acquired pneumonia (underweight, RR 1.8, 95% confidence interval [CI], 1.4-2.2, P < 0.01; overweight, 0.89, 95%CI, 0.8-1.03, P, 0.1; obesity, 1.03, 95% CI, 0.8-1.3, p. 8) and U-shaped relationship between BMI and risk of influenza-related pneumonia (underweight, RR 1.9, 95% CI, 1.2-3, P < 0.01; overweight, 0.89, 95% CI, 0.79-0.99, P, 0.03; obesity, 1.3, 95% CI, 1.05-1.63, p. 2; morbidity obesity, 4.6, 95% CI, 2.2-9.8, P < 0.01); whereas, no difference in risk of nosocomial pneumonia was found across the BMI groups. Gender difference did not make significant contribution in modifying BMI-pneumonia risk relationship.

Transformation of LTP gene into Brassica napus to enhance its resistance to Sclerotinia sclerotiorum

Rapeseed (Brassica napus L.) is one of the most important economic crops worldwide, and Sclerotinia sclerotiorum is the most dangerous disease that affects its yield greatly. Lipid transfer protein (LTP) has broad-spectrum anti-bacterial and fungal activities. In this study, B. napus was transformed using Agrobacterium tumefaciens harboring the plasmid-containing LTP gene to study its possible capability of increasing plant's resistance. First, we optimized the petiole genetic transformation system by adjusting the days of explants, bacterial concentrations, ratio of hormones, and cultivating condition. Second, we obtained 8 positive plants by PCR analysis of T0 generation. The PCR results of T1 generation were positive, indicating that the LTP gene had been integrated into B. napus. Third, T1 transgenic plants inoculated by detached leaves with mycelia of S. sclerotiorum showed better disease resistance than non-transformants. Oxalic acid belongs to secondary metabolites of S. sclerotiorum, and several studies have demonstrated that the resistance of rapeseed to oxalic acid is significantly consistent with its resistance to S. sclerotiorum. The result from the seed germination assay showed that when T1 seeds were exposed to oxalic acid stress, their germination rate was evidently higher than that of non-transformant seeds. In addition, we measured some physiological changes in T1 plants and control plants under oxalic acid stress. The results showed that T1 transgenic plants had lower malondialdehyde (MDA) content, higher super oxide dismutase (SOD), and peroxidase (POD) activities than non-transformants, whereas disease resistance was related to low MDA content and high SOD and POD activities.

SU-E-T-97: Intra and Inter Variability in Beam Data Commissioning among Water Phantom Scanning Systems

PURPOSE

There are many water-phantom scanning systems with advanced features to collect accurate commissioning data. However the intra- and inter-variability of commissioning data has not been reported which is attempted in this study.

METHODS

Four vendors with modern water-phantom scanning systems; PTW, Sun Nuclear (SN), Standard Imaging (SI) and IBA were invited to an institution to demonstrate beam data collection. Each system was used to collect percent depth dose (PDD) and profiles several times in a day with their choice of detector for four different machines for photon and electron beam commissioning. This provided information on intra-variability. At the end, each vendor was allowed to setup and collect data on a single unit for inter-variability. All data were sent to a central location for analysis and evaluation.

RESULTS

The depth dose and profiles for 2×2cm² and 10×10cm² fields were analyzed for intra- and inter-variability. With repeated measurements, the intra-variability provided a detailed degree of fidelity of data collection. This was shown to be with (± 0.1%) among all vendors. Ignoring data in buildup region and comparing with one system (PTW), the PDDs variability were slightly larger 0.02±0.17%, 0.14±0.21%, 0.17±0.2%, for SI, SN and IBA, respectively. The profiles inter-variability in central region were <0.1 %, however in penumbra up to ± 4.8%were observed. The polarity effect was also noted up to 3% which was depth and detector dependent.

CONCLUSIONS

Intra- and inter-variability among various scanning system are very small indicting that all modern systems if used properly could collect data within±0.2% accuracy. The selection of device should be based on institutional comfort and personal preference of software and hardware. This study provides unique opportunity to compare data among systems which is otherwise not possible.

Effects of the mixing ratio of the CaAl12O19:mn and Zn2SiO4:mn color-conversion layer on the color tunable emissions of white organic light-emitting devices

The optical properties of white organic light-emitting devices (WOLEDs) fabricated utilizing a CaAl12O19:Mn and Zn2SiO4:Mn phosphor layer were investigated. X-ray diffraction patterns for CaAl12O19:Mn and Zn2SiO4:Mn phosphors showed that Mn ions in the CaAl12O19:Mn phosphors were completely substituted into Ca ions and that Mn ions in the Zn2SiO4:Mn phosphors were completely substituted into Zn ions. Field emission scanning electron microscopy images showed that the size of the CaAl12O19:Mn phosphor was approximately between 0.1 and 3 microm, and that the size of the Zn2SiO4:Mn phosphor was smaller than 7 microm. The color coordinates of the electroluminescence spectra for WOLEDs with phosphor thicknesses of 0.25 and 0.35 mm shifted to the white emission side because the generated blue light from the blue OLEDs combined with the red and green lights was converted by the CaAl12O19:Mn and the Zn2SiO4:Mn phosphor down-conversion layers.

Generic drug prescriptions following hospital discharge: a prospective study in France

AIMS

Systematic generic prescription at discharge could reduce confusion on drug-name usage, decrease commercial influence on medicine, and reduce drug-related expenditures. This study aimed to analyze generic drug prescriptions at discharge from hospital and to estimate the potential savings associated with a total substitution policy (substitution of every substitutable drug for its cheapest generic counterpart).

METHODS

Drug prescriptions before admission and at discharge of all patients from three medical units of a university hospital were prospectively collected for five weeks without informing prescribers.

RESULTS

Prescriptions from 85 patients were analyzed. On admission, 68 patients (80%) received 413 drugs; 141 were substitutable brand-name drugs and 23 (16%), which were directly prescribed as generics. At discharge, 488 drugs were prescribed to the 85 patients; 180 were substitutable drugs but only 5 (2.8%) were written as generics on prescription pads, a decrease of 78% (p<0.0001) compared to admission. In average, generics were 18% less expensive than brand-name drugs. Some common therapeutic classes offered even greater price difference, such as proton-pump inhibitors (42%), statins (32%), or antihypertensive agents (28%). Potential savings from a total substitution policy at discharge were estimated to €1512 per 1000 patients per week; for lifetime drugs, savings amounted to €18,960 per 1000 patients per year.

CONCLUSIONS

Very few drugs are written as generics on medical forms at discharge in France. Hospital practitioners should be encouraged to prescribe generics, particularly in chronic diseases. A broad generic prescription policy at hospital discharge would result in substantial savings for health insurance.

A review of screening mammography participation and utilization in Canada

Introduction

Participation rate is an important indicator for a screening program’s effectiveness; however, the current approach to measuring participation rate in Canada is not comparable with other countries. The objective of this study is to review the measurement of screening mammography participation in Canada, make international comparisons, and to propose alternative methods.

Methods

Canadian breast cancer screening program data for women aged 50 to 69 years screened between 2004 and 2006 were extracted from the Canadian Breast Cancer Screening Database (CBCSD). The fee-for-services (FSS) mammography data (opportunistic screening mammography) were obtained from the provincial ministries of health. Both screening mammography program participation and utilization were examined over 24 and 30 months.

Results

Canada’s screening participation rate increases from 39.4% for a 24-month cut-off to 43.6% for a 30-month cut-off. The 24-month mammography utilization rate is 63.1% in Canada, and the 30-month utilization rate is 70.4%.

Conclusion

Due to the differences in health service delivery among Canadian provinces, both programmatic participation and overall utilization of mammography at 24 months and 30 months should be monitored.

A review of screening mammography participation and utilization in Canada

INTRODUCTION

Participation rate is an important indicator for a screening program's effectiveness; however, the current approach to measuring participation rate in Canada is not comparable with other countries. The objective of this study is to review the measurement of screening mammography participation in Canada, make international comparisons, and propose alternative methods.

METHODS

Canadian breast cancer screening program data for women aged 50 to 69 years screened between 2004 and 2006 were extracted from the Canadian Breast Cancer Screening Database (CBCSD). The fee-for-services (FSS) mammography data (opportunistic screening mammography) were obtained from the provincial ministries of health. Both screening mammography program participation and utilization were examined over 24 and 30 months.

RESULTS

Canada's screening participation rate increases from 39.4% for a 24-month cut-off to 43.6% for a 30-month cut-off. The 24-month mammography utilization rate is 63.1% in Canada, and the 30-month utilization rate is 70.4%.

CONCLUSION

Due to the differences in health service delivery among Canadian provinces, both programmatic participation and overall utilization of mammography at 24 months and 30 months should be monitored.

HIV-infected patients and treatment outcomes: an equivalence study of community-located, primary care-based HIV treatment vs. hospital-based specialty care in the Bronx, New York

The HIV-infected population in the USA is expanding as patients survive longer and new infections are identified. In many areas, particularly rural/medically underserved regions, there is a growing shortage of providers with sufficient HIV expertise. HIV services incorporated into community-based (CB), primary care settings may therefore improve the distribution and delivery of HIV treatment. Our objective was to describe/compare patients and treatment outcomes in two settings: a community-located, primary care-based HIV program, and a hospital-based (HB) specialty center. CB providers had on-site access to generalist HIV experts. The hospital center was staffed primarily by infectious disease physicians. This was a retrospective cohort study of 854 HIV-positive adults initiating care between 1/2005 and 12/2007 within an academic medical center network in the Bronx, NY. Treatment outcomes were virologic and immunologic response at 16-32 and 48 weeks, respectively, after combination antiretroviral therapy (cART) initiation. We found that HB subjects presented with a higher prevalence of AIDS (59% vs. 46%, p<0.01) and lower initial CD4 (385 vs. 437, p<0.05) than CB subjects. Among 178 community vs. 237 hospital subjects starting cART, 66% vs. 62% achieved virologic suppression (95% confidence interval (CI) difference -0.14-0.06) and 49% vs. 59% achieved immunologic success, defined as a 100 cell/mm³ increase in CD4 (95% CI difference 0.00-0.19). The multivariate-adjusted likelihoods of achieving viral suppression [OR=1.24 (95% CI 0.69-2.33)] and immunologic success [OR=0.76 (95% CI 0.47-1.21)] were not statistically significant for community vs. hospital subjects. Because this was an observational study, propensity scores were used to address potential selection bias when subjects presented to a particular setting. In conclusion, HIV-infected patients initiate care at CB clinics earlier and with less advanced HIV disease. Treatment outcomes are comparable to those at a HB specialty center, suggesting that HIV care can be delivered effectively in community settings.

Emergency Caesarean Section in a Patient with Myotonic Dystrophy: A Case of Failed Postoperative Extubation in a Patient with Mild Disease

A 21-year-old primiparous patient with subclinical myotonic dystrophy presented at a tertiary hospital at 38 weeks gestation in active labour, having previously been reviewed in the high-risk pregnancy clinic. A non-reassuring cardiotocogram and raised foetal scalp lactate necessitated an emergency caesarean section. On extubation following an otherwise unremarkable general anaesthetic, the patient required prompt re-intubation due to respiratory compromise, followed by a more gradual period of weaning from positive pressure ventilation. This review explores the implications of myotonic dystrophy for anaesthesia, discusses its multi-system involvement and highlights the difficulties in identifying at-risk patients in the perioperative setting.

Neutral and acidic oligosaccharides in Holstein-Friesian colostrum during the first 3 days of lactation measured by high performance liquid chromatography on a microfluidic chip and time-of-flight mass spectrometry

Oligosaccharides (OS) from bovine milk are a class of bioactive molecules that are receiving increasing commercial attention for their potential health benefits. In the present work we measured, comprehensively and systematically, free milk OS in the colostrum of 7 Holstein-Friesian cows during the first 3 d of lactation in 12-h intervals by HPLC-chip/time-of-flight mass spectrometry to determine the biological variation of free milk OS in early lactation. The high sensitivity and resolution of the analytical technique made it possible to monitor all OS species, thus providing a comprehensive and quantitative analysis of OS variations during colostrum production. This study confirmed that although sialyllactose is the major OS in bovine colostrum, several neutral OS species are present in significant abundance even at the third day of lactation. Furthermore, variation in terms of OS species and relative abundances of OS between cows suggest individual animal variation. These variations are likely due to genetic factors because environmental factors such as nutrition, lactation number, and accommodation were the same for all cows. This investigation revealed that colostrum milk from Holstein-Friesian cows is a rich source of neutral and acidic OS for the food and pharmaceutical industries.