A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls.

BACKGROUND: Statistical comparison of peptide profiles in biomarker discovery requires fast, user-friendly software for high throughput data analysis. Important features are flexibility in changing input variables and statistical analysis of peptides that are differentially expressed between patient and control groups. In addition, integration the mass spectrometry data with the results of other experiments, such as microarray analysis, and information from other databases requires a central storage of the profile matrix, where protein id's can be added to peptide masses of interest. RESULTS: A new database application is presented, to detect and identify significantly differentially expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The presented modular software is capable of central storage of mass spectra and results in fast analysis. The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, and 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished from those of control groups. CONCLUSION: The database application is capable to distinguish patient Matrix Assisted Laser Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets. The modular architecture of the application makes it possible to adapt the application to handle also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry experiments. It is expected that the higher resolution and mass accuracy of the FT-ICR mass spectrometry prevents the clustering of peaks of different peptides and allows the identification of differentially expressed proteins from the peptide profiles

Prevalence and tracking of back pain from childhood to adolescence

<p>Abstract</p> <p>Background</p> <p>It is generally acknowledged that back pain (BP) is a common condition already in childhood. However, the development until early adulthood is not well understood and, in particular, not the individual tracking pattern. The objectives of this paper are to show the prevalence estimates of BP, low back pain (LBP), mid back pain (MBP), neck pain (NP), and care-seeking because of BP at three different ages (9, 13 and15 years) and how the BP reporting tracks over these age groups over three consecutive surveys.</p> <p>Methods</p> <p>A longitudinal cohort study was carried out from the years of 1997 till 2005, collecting interview data from children who were sampled to be representative of Danish schoolchildren. BP was defined overall and specifically in the three spinal regions as having reported pain within the past month. The prevalence estimates and the various patterns of BP reporting over time are presented as percentages.</p> <p>Results</p> <p>Of the 771 children sampled, 62%, 57%, and 58% participated in the three back surveys and 34% participated in all three. The prevalence estimates for children at the ages of 9, 13, and 15, respectively, were for BP 33%, 28%, and 48%; for LBP 4%, 22%, and 36%; for MBP 20%, 13%, and 35%; and for NP 10%, 7%, and 15%. Seeking care for BP increased from 6% and 8% at the two youngest ages to 34% at the oldest. Only 7% of the children who participated in all three surveys reported BP each time and 30% of these always reported no pain. The patterns of development differed for the three spinal regions and between genders. Status at the previous survey predicted status at the next survey, so that those who had pain before were more likely to report pain again and vice versa. This was most pronounced for care-seeking.</p> <p>Conclusion</p> <p>It was confirmed that BP starts early in life, but the patterns of onset and development over time vary for different parts of the spine and between genders. Because of these differences, it is recommended to report on BP in youngsters separately for the three spinal regions, and to differentiate in the analyses between the genders and age groups. Although only a small minority reported BP at two or all three surveys, tracking of BP (particularly NP) and care seeking was noted from one survey to the other. On the positive side, individuals without BP at a previous survey were likely to remain pain free at the subsequent survey.</p

The evidence base for chiropractic treatment of musculoskeletal conditions in children and adolescents: The emperor's new suit?

Five to ten percent of chiropractic patients are children and adolescents. Most of these consult because of spinal pain, or other musculoskeletal complaints. These musculoskeletal disorders in early life not only affect the quality of children's lives, but also seem to have an impact on adult musculoskeletal health. Thus, this is an important part of the chiropractors' scope of practice, and the objective of this review is to assess the evidence base for manual treatment of musculoskeletal disorders in children and adolescents

Photographic measurement of upper-body sitting posture of high school students: A reliability and validity study

<p>Abstract</p> <p>Background</p> <p>All the reported measures of sitting posture, as well as photographs, have one flaw, as these measures are external to the body. These measures use calculations from external bony landmarks to estimate spinal posture, on the understanding that what is being measured externally reflects the shape, health and performance of structures of the underlying spine. Without a comparative measure of the relative position of the structures of the spine, the validity of any external spinal posture measure cannot be established. This paper reports on a study which tests the validity of photographs to measure adolescent sitting posture.</p> <p>Methods</p> <p>The study was conducted in a laboratory at the Department of Human Biology, University of Cape Town. A random sample of 40 adolescents were recruited from the Cape metropolitan schools, to detect differences of three degrees or more between the repeated measures of upright, normal or slouched posture (photographs) and between the posture photographs and LODOX measures. Eligible participants were healthy male and female subjects aged 15 or 16 years old, in Grade 10, and who were undertaking Computer or Computype studies at their schools. Two posture measurement tools were used in the study, namely: Photographs were taken using the Photographic Posture Analysis Method (PPAM) and Radiograph<it>s </it>were taken using the LODOX (LODOX (Pty) Ltd) system. Subjects' posture was assessed in simulated computer workstations. The following angles were measured: the sagittal head angle, cervical angle, protraction/retraction angle, arm angle and the thoracic angle.</p> <p>Results</p> <p>Data from 39 subjects (19 males, 20 females) was used for analysis (17 15-year-olds (7 boys and 10 girls), 22 16-year-olds (12 boys and 10 girls)). All but one photographic angle showed moderate to good correlation with the LODOX angles (Pearson r values 0.67–0.95) with the exception being the shoulder protraction/retraction angle Pearson r values. Bland Altman limits of agreement illustrated a slight bias for all angles. The reliability study findings from repeated photographs demonstrated moderate to good correlation of all angles (ICC values 0.78–0.99).</p> <p>Conclusion</p> <p>The findings of this study suggest that photographs provide valid and reliable indicators of the position of the underlying spine in sitting. Clinically it is important to know whether a patient is showing true progression in relation to a postural intervention. Based on the results of this study, the PPAM can be used in practice as a valid measure of sitting posture.</p

Metabolic assessment of a novel chronic myelogenous leukemic cell line and an imatinib resistant subline by 1H NMR spectroscopy

The goal of this study was to examine metabolic differences between a novel chronic myelogenous leukemic (CML) cell line, MyL, and a sub-clone, MyL-R, which displays enhanced resistance to the targeted Bcr-Abl tyrosine kinase inhibitor imatinib. 1H nuclear magnetic resonance (NMR) spectroscopy was carried out on cell extracts and conditioned media from each cell type. Both principal component analysis (PCA) and specific metabolite identification and quantification were used to examine metabolic differences between the cell types. MyL cells showed enhanced glucose removal from the media compared to MyL-R cells with significant differences in production rates of the glycolytic end-products, lactate and alanine. Interestingly, the total intracellular creatine pool (creatine + phosphocreatine) was significantly elevated in MyL-R compared to MyL cells. We further demonstrated that the MyL-R cells converted the creatine to phosphocreatine using non-invasive monitoring of perfused alginate-encapsulated MyL-R and MyL cells by in vivo 31P NMR spectroscopy and subsequent HPLC analysis of extracts. Our data demonstrated a clear difference in the metabolite profiles of drug-resistant and sensitive cells, with the biggest difference being an elevation of creatine metabolites in the imatinib-resistant MyL-R cells

Biological traits of European pond macroinvertebrates

Whilst biological traits of river macroinvertebrates show unimodal responses to geographic changes in habitat conditions in Europe, we still do not know whether spatial turnover of species result in distinct combinations of biological traits for pond macroinvertebrates. Here, we used data on the occurrence of 204 macroinvertebrate taxa in 120 ponds from four biogeographic regions of Europe, to compare their biological traits. The Mediterranean, Atlantic, Alpine, and Continental regions have specific climate, vegetation and geology. Only two taxa were exclusively found in the Alpine and Continental regions, while 28 and 34 taxa were exclusively recorded in the Atlantic and Mediterranean regions, respectively. Invertebrates in the Mediterranean region allocated much energy to reproduction and resistance forms. Most Mediterranean invertebrate species had narrow thermal ranges. In Continental areas, invertebrates allocated lesser energy to reproduction and dispersal, and organisms were short lived with high diversity of feeding groups. These characteristics suggest higher resilience. The main difference between ponds in the Alpine and Atlantic regions was their elevation. Alpine conditions necessitate specific adaptations related to rapid temperature fluctuations, and low nutrient concentrations. Even if our samples did not cover the full range of pond conditions across Europe, our analyses suggest that changes in community composition have important impacts on pond ecosystem functions. Consistent information on a larger set of ponds across Europe would be much needed, but their low accessibility (unpublished data and/or not disclosed by authors) remains problematic. There is still, therefore, a pressing need for the incorporation of high quality data sets into a standardized database so that they can be further analyzed in an integrated European-wide manner

Low back pain in 17 year olds has substantial impact and represents an important public health disorder: a cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Prevalence of low back pain (LBP) rises rapidly during adolescence, reaching adult levels by the age of 18. It has been suggested that adolescent LBP is benign with minimal impact, despite limited evidence.</p> <p>Methods</p> <p>The aim of this study was to investigate the impact of LBP and the influence of chronicity, gender and presence of other spinal pain comorbidities at age 17. Subjects (n = 1283) were categorised according to experiencing current and chronic LBP, gender and presence of other areas of spinal pain. LBP impact was ascertained via questions regarding seeking professional assistance, using medication, missing school/work, limited normal or recreational physical activity and health related quality of life (HRQOL).</p> <p>Results</p> <p>12.3% of participants reported current but not chronic LBP, while 19.9% reported current chronic LBP. LBP was more commonly reported by females than males. Other spinal pain comorbidities were common in the LBP groups. Impact was greater in subjects with chronic LBP, in females and in those with other spinal pain comorbidities.</p> <p>Conclusion</p> <p>LBP, and particularly chronic LBP, has a significant negative impact at 17 years. It is commonly associated with care seeking, medication use, school absenteeism, and reduced HRQOL. These findings support that adolescent LBP is an important public health issue that requires attention.</p

Lateral frontal cortex volume reduction in Tourette syndrome revealed by VBM

<p>Abstract</p> <p>Background</p> <p>Structural changes have been found predominantly in the frontal cortex and in the striatum in children and adolescents with Gilles de la Tourette syndrome (GTS). The influence of comorbid symptomatology is unclear. Here we sought to address the question of gray matter abnormalities in GTS patients <it>with </it>co-morbid obsessive-compulsive disorder (OCD) and/or attention deficit hyperactivity disorder (ADHD) using voxel-based morphometry (VBM) in twenty-nine adult actually unmedicated GTS patients and twenty-five healthy control subjects.</p> <p>Results</p> <p>In GTS we detected a cluster of decreased gray matter volume in the left inferior frontal gyrus (IFG), but no regions demonstrating volume increases. By comparing subgroups of GTS with comorbid ADHD to the subgroup with comorbid OCD, we found a left-sided amygdalar volume increase.</p> <p>Conclusions</p> <p>From our results it is suggested that the left IFG may constitute a common underlying structural correlate of GTS with co-morbid OCD/ADHD. A volume reduction in this brain region that has been previously identified as a key region in OCD and was associated with the active inhibition of attentional processes may reflect the failure to control behavior. Amygdala volume increase is discussed on the background of a linkage of this structure with ADHD symptomatology. Correlations with clinical data revealed gray matter volume changes in specific brain areas that have been described in these conditions each.</p