An introduction to low-level analysis methods of DNA microarray data

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of nucleic acid abundance in a set of tissues or cell populations for thousands of transcripts or loci simultaneously. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. This includes the design of probes, the experimental design, the image analysis of microarray scanned images, the normalization of fluorescence intensities, the assessment of the quality of microarray data and incorporation of quality information in subsequent analyses, the combination of information across arrays and across sets of experiments, the discovery and recognition of patterns in expression at the single gene and multiple gene levels, and the assessment of significance of these findings, considering the fact that there is a lot of noise and thus random features in the data. For all of these components, access to a flexible and efficient statistical computing environment is an essential aspect.

Anaesthesia for castration of piglets: comparison between intranasal and intramuscular application of ketamine, climazolam and azaperone

The aim of this study was to compare the effect of an anaesthetic combination given either intramuscularly (IM) or intranasally (IN) for castration of piglets. Forty piglets aged 4 to 7 days were randomly assigned to receive a mixture of ketamine 15 mg kg-1, climazolam 1.5 mg kg-1 and azaperone 1.0 mg kg-1, IN or IM, 10 minutes prior to castration. Physiological parameters were measured. Castration was videotaped for evaluation by 3 independent observers using a scoring system. Reaction and vocalization to the skin incision and cutting of spermatic cord was evaluated and scored (0 = no reaction, 16 = strong reaction). The IN group had a significantly higher (P < 0.01) castration score, compared to the IM group. There was an association between castration score and room temperature in the IN group (with temperatures below 18 "C associated with a higher castration scores (P < 0.001). Heart rate was significantly higher 10 minutes after castration in the IN group (P < 0.05). Respiratory rate was significantly higher in the IM group at time points -5, -1, 10, 20 and 30 (P < 0.05).The IN group was walking significantly (P < 0.0001) faster than the IM group. In conclusion, this combination provides effective anaesthesia for routine castration of newborn piglets when administered IM. IN administration provided shorter recovery times but had significantly higher castration scores.

Monte Carlo calculation of Varian 2300C/D Linac photon beam characteristics: a comparison between MCNP4C, GEANT3 and measurements

Different codes are used for Monte Carlo (MC) calculations in radiation therapy. In this research, MCNP4C and GEANT3 codes have been compared in calculations of dosimetric characteristics of Varian Clinac 2300C/D. The parameters of influence in the differences seen in dosimetric features were discussed. This study emphasizes that both MCNP4C and GEANT3 MC can be used in radiation therapy computations and their differences in photon spectra calculations have a negligible effect on percentage depth dose computations in radiation therapy.

Periprocedural embolic events related to carotid artery stenting detected by diffusion-weighted MRI: comparison between proximal and distal embolus protection devices

PURPOSE: To evaluate and compare the efficacy of proximal versus distal embolus protection devices (EPD) during carotid artery angioplasty/stenting (CAS) based on diffusion-weighted magnetic resonance imaging (DW-MRI). METHODS: Forty-four patients (31 men; mean age 68 years, range 48-85) underwent protected CAS and had DW-MRI before and after the intervention. The cohort was analyzed according to the type of EPD used: a proximal EPD was deployed in 25 (56.8%) patients (17 men; mean age 66 years, range 48-85) and a distal filter in 19 (14 men; mean age 70 years, range 58-79). Fifteen (60.0%) patients with proximal protection were symptomatic of the target lesion; in the distal protection group, 10 (52.6%) were symptomatic. RESULTS: New lesions were seen on the postinterventional DW-MRI in 28.0% (7/25) of the proximal EPD group versus 32.6% (6/19) of those with a distal filter (p = NS). The majority were clinically silent. The new lesions in the vascular territory of the stented carotid artery in the group as a whole and per patient were fewer in the proximal EPD group (p = NS). No significant differences were noted in the T(2) appearance of the new lesions or the number of new lesions observed away from the vascular territory of the stented artery. CONCLUSION: Proximal embolus protection devices show a nonsignificant trend toward fewer embolic events, which warrants large-scale studies. Furthermore, proximal protection devices can be useful to control and treat acute in-stent thrombosis.

Patients motives for choosing a physician: Comparison between conventional and complementary medicine in Swiss primary care

Background The study is part of a nationwide evaluation of complementary and alternative medicine (CAM) in primary care in Switzerland. The Objective was to identify patients' expectations and reasons governing the choice of complementary medicine compared with conventional primary care (CONV). Methods The data were derived from the PEK study (Programm Evaluation Komplementärmedizin), which was conducted in 2002–2003 with 7879 adult patients and parents of 1291 underage patients, seeking either complementary (CAM) or conventional (CONV) primary care. The study was performed as a cross-sectional survey. The respondents were asked to document their (or their children's) self-perceived health status, reasons governing their choice, and treatment expectations. Physicians were practicing conventional medicine and/or complementary methods (homeopathy, anthroposophic medicine, neural therapy, and traditional Chinese medicine). Reasons governing the choice of physician were evaluated on the basis of a three-part classification (physician-related, procedure-related, and pragmatic/other reasons) Results and Discussion Patients seeing CAM physicians tend to be younger and more often female. CAM patients referred to procedure-related reasons more frequently, whereas pragmatic reasons dominated among CONV patients. CAM respondents expected fewer adverse side effects compared to conventional care patients. Conclusion The majority of alternative medicine users appear to have chosen CAM mainly because they wish to undergo a certain procedure; additional reasons include desire for more comprehensive treatment, and expectation of fewer side-effects.

Managerial perseptions on corporate social responsbility: A Transatlantic comparison between forest products companies in Europe and North America

Corporate Social Responsibility (CSR) addresses the responsibility of companies for their impacts on society. The concept of strategic CSR is becoming increasingly mainstreamed in the forest industry, but there is, however, little consensus on the definition and implementation of CSR. The objective of this research is to build knowledge on the characteristics of CSR and to provide insights on the emerging trend to increase the credibility and legitimacy of CSR through standardization. The study explores how the sustainability managers of European and North American forest companies perceive CSR and the recently released ISO 26000 guidance standard on social responsibility. The conclusions were drawn from an analysis of two data sets; multivariate survey data based on one subset of 30 European and 13 North American responses, and data obtained through in-depth interviewing of 10 sustainability managers that volunteered for an hour long phone discussion about social responsibility practices at their company. The analysis concluded that there are no major differences in the characteristics of cross-Atlantic CSR. Hence, the results were consistent with previous research that suggests that CSR is a case- and company-specific concept. Regarding the components of CSR, environmental issues and organizational governance were key priorities in both regions. Consumer issues, human rights, and financial issues were among the least addressed categories. The study reveals that there are varying perceptions on the ISO 26000 guidance standard, both positive and negative. Moreover, sustainability managers of European and North American forest companies are still uncertain regarding the applicability of the ISO 26000 guidance standard to the forest industry. This study is among the first to provide a preliminary review of the practical implications of the ISO 26000 standard in the forest sector. The results may be utilized by sustainability managers interested in the best practices on CSR, and also by a variety of forest industrial stakeholders interested in the practical outcomes of the long-lasting CSR debate.

Comparing remote sensing and ground-based methods of quantifying cover type and carbon storage in an urban forest

Understanding the canopy cover of an urban environment leads to better estimates of carbon storage and more informed management decisions by urban foresters. The most commonly used method for assessing urban forest cover type extent is ground surveys, which can be both timeconsuming and expensive. The analysis of aerial photos is an alternative method that is faster, cheaper, and can cover a larger number of sites, but may be less accurate. The objectives of this paper were (1) to compare three methods of cover type assessment for Los Angeles, CA: handdelineation of aerial photos in ArcMap, supervised classification of aerial photos in ERDAS Imagine, and ground-collected data using the Urban Forest Effects (UFORE) model protocol; (2) to determine how well remote sensing methods estimate carbon storage as predicted by the UFORE model; and (3) to explore the influence of tree diameter and tree density on carbon storage estimates. Four major cover types (bare ground, fine vegetation, coarse vegetation, and impervious surfaces) were determined from 348 plots (0.039 ha each) randomly stratified according to land-use. Hand-delineation was better than supervised classification at predicting ground-based measurements of cover type and UFORE model-predicted carbon storage. Most error in supervised classification resulted from shadow, which was interpreted as unknown cover type. Neither tree diameter or tree density per plot significantly affected the relationship between carbon storage and canopy cover. The efficiency of remote sensing rather than in situ data collection allows urban forest managers the ability to quickly assess a city and plan accordingly while also preserving their often-limited budget.

Comparison between confocal scanning laser tomography, scanning laser polarimetry and optical coherence tomography on the ability to detect localised retinal nerve fibre layer defects in glaucoma patients

BACKGROUND/AIM: To compare the ability of confocal scanning laser tomography (CSLT), scanning laser polarimetry (SLP) and optical coherence tomography (OCT) in recognising localised retinal nerve fibre layer (RNFL) defects. METHODS: 51 eyes from 43 patients with glaucoma were identified by two observers as having RNFL defects visible on optic disc photographs. 51 eyes of 32 normal subjects were used as controls. Three masked observers evaluated CSLT, SLP and OCT images to determine subjectively the presence of localised RNFL defects. RESULTS: Interobserver agreement was highest with OCT, followed by SLP and CSLT (mean kappa: 0.83, 0.69 and 0.64, respectively). RNFL defects were identified in 58.8% of CSLT, 66.7% of SLP and 54.9% of OCT (p = 0.02 between SLP and OCT) by at least two observers. In the controls, 94.1% of CSLT, 84.3% of SLP and 94.1% of OCT scans, respectively, were rated as normal (p = 0.02 between CSLT and SLP, and SLP and OCT). CONCLUSION: Approximately 20-40% of localised RNFL defects identified by colour optic disc photographs are not detected by CSLT, SPL or OCT. SLP showed a higher number of false-positive results than the other techniques, but also had a higher proportion of correctly identified RNFL defects in the glaucoma population.

Comparison between intravitreal and orbital floor triamcinolone acetonide after phacoemulsification in patients with endogenous uveitis

PURPOSE: To compare the effect of intravitreal and orbital floor triamcinolone acetonide (TA) on macular edema, visual outcome, and course of postoperative inflammation after cataract surgery in uveitis patients. DESIGN: Prospective, randomized clinical trial. METHODS: Monocenter study (40 patients) with chronic endogenous uveitis who underwent phacoemulsification with intraocular lens implantation with either 4 mg intravitreal TA (n = 20) or 40 mg orbital floor TA (n = 20). The primary outcome was influence on cystoid macular edema (CME). Secondary outcome measures were best-corrected visual acuity (BCVA), anterior chamber cell grade, laser flare photometry, giant cell deposition, posterior capsule opacification (PCO), and intraocular pressure. RESULTS: Mean central foveal thickness decreased in the intravitreal TA group and increased in the orbital floor TA group (P < .001 at one and three months). CME improved in 50% of patients after intravitreal TA, whereas it was unchanged after orbital floor TA (difference between the groups at three months, P = .049). Mean BCVA (logarithm of the minimal angle of resolution) improved postoperatively (P < .001) from 0.76 and 0.74 to 0.22 and 0.23 in the intravitreal TA and orbital floor TA group, respectively. Anterior chamber cell count at one month was lower in the intravitreal TA than in the orbital floor TA group (P = .02). Laser flare photometry values and giant cell numbers were slightly higher after orbital floor TA than after intravitreal TA. The groups did not differ with respect to PCO rate and ocular hypertension. CONCLUSIONS: The CME improvement and anti-inflammatory effect after intravitreal TA was better than after orbital floor TA injection in cataract surgery in uveitis patients.

Thermal plasticity of mitochondria: a latitudinal comparison between Southern Ocean molluscs

Mitochondrial volume density (Vv((mt,f))), cristae surface density (Sv((im,mt))), cristae surface area (Sv((im,f))) and citrate synthase (CS) activity were analysed as indicators of thermal acclimation in foot muscle of the limpet, Nacella concinna, and the clam, Laternula elliptica, collected from 4 locations within the Southern Ocean, South Georgia (54 degrees S, N. concinna only), Signy (60 degrees S), Jubany (L. elliptica only -62 degrees S) and Rothera (67 degrees S). Animals were acclimated to 0.0 degrees C whilst a sub-set of N. concinna (South Georgia, Signy and Rothera) and L. elliptica (Rothera) were acclimated to 3.0 degrees C. At 0.0 degrees C N. concinna had higher Vv((mt,f)), Sv((im,mt)), Sv((im,f)) and muscle fibre specific CS activity than L. elliptica which correlated with the more active life style of N. concinna. However, mitochondrial density was very low, 1-2% in both species, suggesting that low temperature compensation of mitochondrial density is not a universal evolutionary response of Antarctic marine ectotherms. Both Sv((im,mt)) and Sv((im,f)) were reduced by warm acclimation of N. concinna. South Georgia N. concinna maintained muscle fibre specific CS activity after acclimation, in contrast to N. concinna from Rothera and Signy and L. elliptica from Rothera, indicating that they have the physiological plasticity to respond to their warmer, more variable thermal environment.

A comparison between two-dimensional and three-dimensional cephalometry on frontal radiographs and on cone beam computed tomography scans of human skulls

The aim of this study was to evaluate whether measurements performed on conventional frontal radiographs are comparable to measurements performed on three-dimensional (3D) models of human skulls derived from cone beam computed tomography (CBCT) scans and if the latter can be used in longitudinal studies. Cone beam computed tomography scans and conventional frontal cephalometric radiographs were made of 40 dry human skulls. From the CBCT scan a 3D model was constructed. Standard cephalometric software was used to identify landmarks and to calculate ratios and angles. The same operator identified 10 landmarks on both types of cephalometric radiographs, and on all images, five times with a time interval of 1 wk. Intra-observer reliability was acceptable for all measurements. There was a statistically significant and clinically relevant difference between measurements performed on conventional frontal radiographs and on 3D CBCT-derived models of the same skull. There was a clinically relevant difference between angular measurements performed on conventional frontal cephalometric radiographs, compared with measurements performed on 3D models constructed from CBCT scans. We therefore recommend that 3D models should not be used for longitudinal research in cases where there are only two-dimensional (2D) records from the past.