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1.  Immunodepletion of high-abundant proteins from acute and chronic wound fluids to elucidate low-abundant regulators in wound healing 
BMC Research Notes  2010;3:335.
Background
The process of wound healing consists of several well distinguishable and finely tuned phases. For most of these phases specific proteins have been characterized, although the underlying mechanisms of regulation are not yet fully understood. It is an open question as to whether deficits in wound healing can be traced back to chronic illnesses such as diabetes mellitus. Previous research efforts in this field focus largely on a restricted set of marker proteins due to the limitations detection by antibodies imposes. For mechanistic purposes the elucidation of differences in acute and chronic wounds can be addressed by a less restricted proteome study. Mass spectrometric (MS) methods, e.g. multi dimensional protein identification technology (MudPIT), are well suitable for this complex theme of interest. The human wound fluid proteome is extremely complex, as is human plasma. Therefore, high-abundant proteins often mask the mass spectrometric detection of lower-abundant ones, which makes a depletion step of such predominant proteins inevitable.
Findings
In this study a commercially available immunodepletion kit was evaluated for the detection of low-abundant proteins from wound fluids. The dynamic range of the entire workflow was significantly increased to 5-6 orders of magnitude, which makes low-abundant regulatory proteins involved in wound healing accessible for MS detection.
Conclusion
The depletion of abundant proteins is absolutely necessary in order to analyze highly complex protein mixtures such as wound fluids using mass spectrometry. For this the used immunodepletion kit is a first but important step in order to represent the entire dynamic range of highly complex protein mixtures in the future.
doi:10.1186/1756-0500-3-335
PMCID: PMC3020179  PMID: 21156046
2.  A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication 
BMC Research Notes  2010;3:235.
BMC Research Notes aims to ensure that data files underlying published articles are made available in standard, reusable formats, and the journal is calling for contributions from the scientific community to achieve this goal. Educational Data Notes included in this special series should describe a domain-specific data standard and provide an example data set with the article, or a link to data that are permanently hosted elsewhere. The contributions should also provide some evidence of the data standard's application and preparation guidance that could be used by others wishing to conduct similar experiments. The journal is also keen to receive contributions on broader aspects of scientific data sharing, archiving, and open data.
doi:10.1186/1756-0500-3-235
PMCID: PMC2940773  PMID: 20813027
3.  Genotypic and phenotypic variation among Staphylococcus saprophyticus from human and animal isolates 
BMC Research Notes  2010;3:163.
Background
The main aim of this study was to examine the genotypic and phenotypic diversity of Staphylococcus saprophyticus isolates from human and animal origin.
Findings
In total, 236 clinical isolates and 15 animal isolates of S. saprophyticus were characterized in respect of the occurrence of 9 potential virulence genes and four surface properties. All strains were PCR positive for the regulatory genes agr, sar >it>A and rot as well as for the surface proteins UafA and Aas. Nearly 90% of the clinical isolates were found to possess the gene for the surface-associated lipase Ssp and 10% for the collagen binding MSCRAMM SdrI. All animal isolates were negative forsdrI. Lipolytic activity could be detected in 66% of the clinical and 46% of the animal isolates. Adherence to collagen type I was shown of 20% of the clinical strains and 6% of the strains of animal origin. Most S. saprophyticus strains showed hydrophobic properties and only few could agglutinate sheep erythrocytes.
Conclusions
We described a broad analysis of animal and human S. saprophyticus isolates regarding virulence genes and phenotypic properties such as lipase activity, hydrophobicity, and adherence. While S. saprophyticus strains from animal sources have prerequisites for colonization of the urinary tract like the D-serine-deaminase, out findings suggested that they need to acquire new genes e.g. MSCRAMMS for adherence like sdrI and to modulate their existing properties e.g. increasing the lipase activity or reducing hydrophobicity. These apparently important new genes or properties for virulence have to be further analyzed.
doi:10.1186/1756-0500-3-163
PMCID: PMC2901211  PMID: 20537181
4.  AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm 
BMC Research Notes  2010;3:117.
Background
Epistatic interactions of multiple single nucleotide polymorphisms (SNPs) are now believed to affect individual susceptibility to common diseases. The detection of such interactions, however, is a challenging task in large scale association studies. Ant colony optimization (ACO) algorithms have been shown to be useful in detecting epistatic interactions.
Findings
AntEpiSeeker, a new two-stage ant colony optimization algorithm, has been developed for detecting epistasis in a case-control design. Based on some practical epistatic models, AntEpiSeeker has performed very well.
Conclusions
AntEpiSeeker is a powerful and efficient tool for large-scale association studies and can be downloaded from http://nce.ads.uga.edu/~romdhane/AntEpiSeeker/index.html.
doi:10.1186/1756-0500-3-117
PMCID: PMC2880958  PMID: 20426808
5.  Normative scores for a brief neuropsychological battery for the detection of HIV-associated neurocognitive disorder (HAND) among South Africans 
BMC Research Notes  2010;3:28.
Background
There is an urgent need to more accurately diagnose HIV-associated neurocognitive disorder (HAND) in Africa. Rapid screening tests for HIV-associated dementia are of limited utility due to variable sensitivity and specificity. The use of selected neuropsychological tests is more appropriate, but norms for HIV seronegative people are not readily available for sub-Saharan African populations. We sought to derive normative scores for two commonly used neuropsychological tests that generate four test scores -- namely the Trail-Making Test (Parts A and B) and the Digit Span Test [Forward (DSF) and Backward (DSB)]. To assess memory and recall, we used the memory item of the International HIV Dementia Scale (IHDS).
Findings
One hundred and ten HIV seronegative participants were assessed at McCord Hospital, Durban, South Africa between March 3rd and October 31st, 2008. We excluded people with major depressive disorder, substance use abuse and dependence and head injuries (with or without loss of consciousness). All the participants in this study were African and predominantly female with an average age of 28.5 years and 10 years of education. Age and gender influenced neuropsychological functioning, with older people performing worse. The effect of gender was not uniform across all the tests.
Conclusion
These two neuropsychological tests can be administered with the IHDS in busy antiretroviral clinics. Their performance can be measured against these norms to more accurately diagnose the spectrum and progression of HAND.
doi:10.1186/1756-0500-3-28
PMCID: PMC2843737  PMID: 20181051
6.  Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays 
BMC Research Notes  2010;3:350.
Background
The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarrays. The method is based on a Bayesian spatial normal mixture model with an unknown number of components corresponding to true copy numbers. A reversible jump Markov chain Monte Carlo algorithm is used to implement the model and perform posterior inference.
Results
The performance of the algorithm is examined on both simulated and real cancer data, and it is compared with the popular CNAG algorithm for copy number detection.
Conclusions
We demonstrate that our Bayesian mixture model performs at least as well as the hidden Markov model based CNAG algorithm and in certain cases does better. One of the added advantages of our method is the flexibility of modeling normal cell contamination in tumor samples.
doi:10.1186/1756-0500-3-350
PMCID: PMC3023756  PMID: 21192799
7.  Exploring the use of internal and externalcontrols for assessing microarray technical performance 
BMC Research Notes  2010;3:349.
Background
The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies.
Results
A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes") was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification). External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC) metrics.
Conclusions
These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray experiments. The observed consistency amongst the information carried by internal and external controls and whole-array quality measures offers promise for rationally-designed control standards for routine performance monitoring of multiplexed measurement platforms.
doi:10.1186/1756-0500-3-349
PMCID: PMC3020182  PMID: 21189145
8.  Antimicrobial resistance among producers and non-producers of extended spectrum beta-lactamases in urinary isolates at a tertiary Hospital in Tanzania 
BMC Research Notes  2010;3:348.
Background
Published data on the existence and magnitude of extended spectrum beta-lactamase (ESBL) production in urinary pathogens in local setting is limited. The aim of the present study was to determine the prevalence of antimicrobial resistance and ESBL production among Escherichia coli and Klebsiella spp from urine samples in a tertiary hospital. This was a cross sectional study conducted at Muhimbili National Hospital in Dar es Salaam, Tanzania.
Findings
A total of 270 E.coli and Klebsiella spp urinary pathogens from children and adults isolated from January to March 2010 were included in the study. E. coli and Klebsiella spp isolates were tested for antimicrobial susceptibility by the Clinical and Laboratory Standard Institute's disc diffusion method. These isolates were further screened for ESBL phenotype using cefotaxime and ceftazidime discs. Isolates with reduced sensitivity were confirmed using ESBL E-test strips. Of 270 isolates, 138 (51.1%) were E. coli and 132 (48.9%) were Klebsiella spp. ESBL was detected in 122 (45.2%) of all the isolates. ESBL- producing E. coli strains were significantly more resistance to cotrimoxazole (90.7%), ciprofloxacin (46.3%) and nalidixic acid (61.6%) than strains that did not produce ESBL (p < 0.05). Similarly, ESBL- producing Klebsiella spp strains were significantly more resistance to cotrimoxazole (92.6%), ciprofloxacin (25.0%), nalidixic acid (66.2%), and gentamicin (38.2%) than strains that did not produce ESBL (P < 0.05). Multi-drug resistance was found to be significantly (P < 0.05) more in ESBL producing isolates (90.5%) than non ESBL producers (68.9%). The occurrence of ESBL was significantly higher among isolates from inpatients than outpatients [95 (50.5%) vs. 27(32.9%)] (p = 0.008). The occurrence of ESBL was significantly higher among isolates from children than in adults [84 (54.9%) vs. 38(32.5%)] (p < 0.001).
Conclusions
High prevalence of ESBL-producing E. coli and Klebsiella spp strains was found among inpatients and children. Most of the ESBL- producing isolates were multi-drug resistant making available therapeutic choices limited. We recommend continued antibiotic surveillance as well comprehensive multi-center studies to address the emerging problem of ESBL-associated infections in order to preserve the continued usefulness of most antimicrobial drugs. Further more conducting molecular studies will help to evaluate the various ESBL types.
doi:10.1186/1756-0500-3-348
PMCID: PMC3017072  PMID: 21184671
9.  Impact on cell to plasma ratio of miR-92a in patients with acute leukemia: in vivo assessment of cell to plasma ratio of miR-92a 
BMC Research Notes  2010;3:347.
Background
Plasma microRNA (miRNA) has become a promising biomarker for detecting cancer; however, it remains uncertain whether miRNA expression levels in plasma reflect those in tumor cells. Our aim was to determine the biological relevance of miR-92a, which has been implicated as an oncomiR in both plasma and leukemia cells in patients with acute leukemia and to evaluate whether it could be a novel biomarker for monitoring these patients.
Results
We quantified the expression level of miR-92a in both cells and plasma by reverse transcription polymerase chain reaction in 91 patients with acute leukemia. We also determined miR-92a expression levels in peripheral blood mononuclear cells (PBMNC) from normal controls. We compared miR-92a expression in plasma with its expression in leukemia cells. Synthetic anti-miR-92a inhibitor was transfected into Raji and OM9;22 cells, and apoptosis was assessed. For in vivo assessment, 6-week-old female nude mice were injected with U937 cells, and miR-92a expression in plasma and tumors was measured. The level of miR-92a expression in fresh leukemia cells was highly variable compared with PBMNC, but significantly lower compared with CD34-positive cells obtained from healthy volunteers. We also noticed that miR-92a was preferentially expressed in acute lymphoblastic leukemia (ALL) cells in comparison with acute myeloid leukemia (AML) cells. More specifically, cellular miR-92a expression was significantly increased in a subset of ALL cells, and ALL patients with overexpressed miR-92a had poor prognoses. The anti-miR-92a inhibitor-treated Raji and OM9;22 cells revealed an increase of apoptotic cells. Notably, the cell to plasma ratio of miR-92a expression was significantly higher in both AML and ALL cells compared with PBMNC from healthy volunteers. In tumor-bearing mice, the plasma miR-92a level was significantly decreased in accordance with tumor growth, while tumor tissue was strongly positive for miR-92a.
Conclusions
The miR-92a expression in leukemia cells could be a prognostic factor in ALL patients. The inverse correlation of miR-92a expression between cells and plasma and the cell to plasma ratio may be important to understanding the clinical and biological relevance of miR-92a in acute leukemia.
doi:10.1186/1756-0500-3-347
PMCID: PMC3022817  PMID: 21182798
10.  Investigating effects of parasite infection on body condition of the Kafue lechwe (Kobus leche kafuensis) in the Kafue basin 
BMC Research Notes  2010;3:346.
Background
The Kafue lechwe (Kobus leche Kafuensis), a medium-sized semi-aquatic antelope, is endemic to the Kafue basin of Zambia. The population of the Kafue lechwe has significantly dropped in the last decades leading to its subsequent inclusion on the red list of endangered species. In order to save the remaining population from extinction, it has become increasingly important that the impact of parasite infection and infestation on the Kafue lechwe is investigated.
Findings
Endoparasites accounted for the majority of parasites observed from a study of 40 Kafue lechwe occurring in the the Kafue basin. Amphistoma spp. were present in all animals examined, while Fasciola gigantica had a prevalence rate of 0.525 (95% CI: 0.36 to 0.69) and species of Schistosoma 0.3 (95% CI: 0.15 to 0.45). Among the ectoparasites, Strobiloestrous vanzyli, had a prevalence rate of 0.15 (95% CI: 0.03 to 0.27), while Rhipicephalus appendiculatus had a prevalence of 0.075 (3/40). Our findings indicate that body condition was not influenced by the parasitic infestation in Kafue lechwe. There was no association between sex and parasitic burden (odds ratio = 0.3, 95% CI: 0.8-1.3). However, an association between age and parasitic burden was observed as older animals above 15 years were more likely to get parasite infections than those aged between 1-5 years (odds ratio = 1.5, 95% CI: 1.1-2.4).
Conclusion
Overall, there was no evidence that parasitic infections and infestations adversely affected the lechwe population on the Kafue basin. These findings indicate that ecto- and endo-parasite infestation might not play a significant role in reducing the Kafue lechwe population on the Kafue basin.
doi:10.1186/1756-0500-3-346
PMCID: PMC3017071  PMID: 21182793
11.  Hydrophobins from Aspergillus species cannot be clearly divided into two classes 
BMC Research Notes  2010;3:344.
Background
Hydrophobins are a family of small secreted proteins with a characteristic pattern of eight cysteine residues found exclusively in filamentous fungi. They have originally been divided into two classes based on their physical properties and hydropathy patterns, and are involved in the attachment of hyphae to hydrophobic structures, the formation of aerial structures and appear to be involved in pathogenicity.
Findings
Analysis of nine genome sequences from seven Aspergilli revealed fifty hydrophobins, where each species displayed between two to eight hydrophobins. Twenty of the identified hydrophobins have not previously been described from these species. Apart from the cysteines, very little amino acid sequence homology was observed. Twenty-three of the identified hydrophobins could be classified as class I hydrophobins based on their conserved cysteine spacing pattern and hydropathy pattern. However twenty-six of the identified hydrophobins were intermediate forms. Notably, a single hydrophobin, ATEG_04730, from Aspergillus terreus displayed class II cysteine spacing and had a class II hydropathy pattern.
Conclusion
Fifty hydrophobins were identified in Aspergillus, all containing the characteristic eight cysteine pattern. Aspergillus terreus exhibited both class I and class II hydrophobins. This is the first report of an Aspergillus species with the potential to express both class I and class II hydrophobins. Many of the identified hydrophobins could not directly be allocated to either class I or class II.
doi:10.1186/1756-0500-3-344
PMCID: PMC3020181  PMID: 21182770
12.  Up to seven-fold inter-hospital differences in obstetric anal sphincter injury rates- A birth register-based study in Finland 
BMC Research Notes  2010;3:345.
Background
The occurrence of obstetric anal sphincter injuries (OASIS) - which may have serious, long-term effects on affected women, including faecal incontinence, despite primary repair - varies widely between countries and have been chosen one of the indicators for patient safety in Organisation for Economic Cooperation and Development (OECD) countries and in Nordic countries.
Findings
The aim of the study was to assess risks of OASIS among five university teaching hospitals and 14 non-university central hospitals with more than 1,000 deliveries annually during 1997-2007 in Finland. Women with singleton vaginal deliveries divided into two populations consisting of all 168,637 women from five university hospitals and all 255,660 women from non-university hospitals, respectively, derived from population-based register. Primiparous and multiparous women with OASIS (n = 2,448) were compared in terms of possible risk factors to primiparous and multiparous women without OASIS, respectively, using stepwise logistic regression analysis. The occurrences of OASIS varied from 0.7% to 2.1% in primiparous and from 0.1% to 0.3% in multiparous women among the university hospitals. Three-fold inter-hospital differences in OASIS rates did not significantly change after adjustment for patient mix or the use of interventions. In non-university hospitals OASIS rates varied from 0.2% to 1.4% in primiparous and from 0.02% to 0.4% in multiparous women, and the results remained virtually unchanged after adjustment for known risks.
Conclusions
Up to 3.2-fold inter-hospital differences in OASIS risk demonstrates significant differences in the quality of Finnish obstetric care.
doi:10.1186/1756-0500-3-345
PMCID: PMC3022816  PMID: 21182773
13.  Analysis of Escherichia coli O157 clinical isolates by multilocus sequence typing 
BMC Research Notes  2010;3:343.
Background
Although many strain typing methods exist for pathogenic Escherichia coli, most have drawbacks in terms of resolving power, interpretability, or scalability. For this reason, multilocus sequence typing (MLST) is an appealing alternative especially when applied to the typing of temporal and spatially separated isolates. This method relies on an unambiguous DNA sequence analysis of nucleotide polymorphisms in housekeeping genes and has shown a high degree of intraspecies discriminatory power for bacterial and fungal pathogens.
Results
Here we used the MLST method to study the genetic diversity among E. coli O157 isolates collected from humans from two different locations of USA over a period of several years (2000-2008). MLST analysis of 33 E. coli O157 patient isolates using the eBurst algorithm distinguished 26 different sequence types (STs), which were clustered into two clonal groups and 11 singletons. The predominant ST was ST2, which consisted of 5 isolates (14.28%) followed by ST1 (11.42%). All the isolates under clonal group I exhibited a virtually similar virulence profile except for two strains, which tested negative for the presence of stx genes. The isolates that were assigned to clonal group II in addition to the 11 singletons were found to be phylogenetically distant from clonal group I. Furthermore, we observed a positive correlation between the virulence profile of the isolates and their clonal origin.
Conclusions
Our data suggests the presence of genetic diversity among E. coli O157 isolates from humans shows no measurable correlation to the geographic origin of the isolates.
doi:10.1186/1756-0500-3-343
PMCID: PMC3016269  PMID: 21176142
14.  Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia 
BMC Research Notes  2010;3:341.
Background
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the western population. Although genetic factors are considered to contribute to CLL etiology, at present genomic aberrations identified in CLL are limited compared with those identified in other types of leukemia, which raises the question of the degree of genetic influence on CLL. We performed a high-resolution genome scanning study to address this issue.
Findings
Using the restriction paired-end-based Ditag Genome Scanning technique, we analyzed three primary CLL samples at a kilobase resolution, and further validated the results in eight primary CLL samples including the two used for ditag collection. From 51,632 paired-end tags commonly detected in the three CLL samples representing 5% of the HindIII restriction fragments in the genomes, we identified 230 paired-end tags that were present in all three CLL genomes but not in multiple normal human genome reference sequences. Mapping the full-length sequences of the fragments detected by these unmapped tags in seven additional CLL samples confirmed that these are the genomic aberrations caused by small insertions and deletions, and base changes spreading across coding and non-coding regions.
Conclusions
Our study identified hundreds of loci with insertion, deletion, base change, and restriction site polymorphism present in both coding and non-coding regions in CLL genomes, indicating the wide presence of small genomic aberrations in chronic lymphocytic leukemia. Our study supports the use of a whole genome sequencing approach for comprehensively decoding the CLL genome for better understanding of the genetic defects in CLL.
doi:10.1186/1756-0500-3-341
PMCID: PMC3016268  PMID: 21172017
15.  Illness costs to households are a key barrier to access diagnostic and treatment services for tuberculosis in Tajikistan 
BMC Research Notes  2010;3:340.
Background
Tuberculosis (TB) control is based on early detection and complete treatment of infectious cases. Consequently, it is important that TB suspects and patients can readily access medical care. This qualitative study investigated determinants of access to DOTS services as identified by patients, health providers and community members in four districts in Tajikistan.
Findings
Focus group discussions were conducted in order to investigate access to TB services. A conceptual framework for access to care guided the analysis. Thirteen focus group discussions involving a total of 97 informants were conducted. Content analysis of discussions and a rating to quantify the relative importance of discussed factors were carried out. The conceptual framework identifies five main components of access to which factors can be assigned: availability, adequacy, acceptability, accessibility and affordability.
Financial factors were considered the most important determinants of access to diagnosis and treatment of tuberculosis. Expenditure for drugs and consultations, for transport, and for special foods as well as lost income were identified as major barriers to treatment. Stigma, doubts about curability and low perceived quality of care were not seen to be significant determinants of access to care for tuberculosis. Community members were well aware of symptoms of tuberculosis and of medical services. These findings were consistent between different respondent groups (community members, patients and providers). They were also highly consistent between the open discussion and the confidential rating.
Conclusions
Illness-costs to households were identified as the main barrier to tuberculosis diagnosis and treatment. To improve access and ultimately adherence to tuberculosis treatment, effective mitigation strategies, e.g. changes in case management, food contributions or financial stimuli, need to be explored and implemented.
doi:10.1186/1756-0500-3-340
PMCID: PMC3022814  PMID: 21172015
16.  Text messaging: an innovative method of data collection in medical research 
BMC Research Notes  2010;3:342.
Background
The ubiquitous use of mobile phones in sending and receiving text messages has become a norm for young people. Undeniably, text messaging has become a new and important communication medium not only in the social realm but in education as well. The aim of this study is to evaluate the effectiveness of using text messaging as a means to collect data for a medical research project.
A cross sectional study was carried out during a double blind, randomized controlled trial to assess the efficacy and safety of a probiotic in the management of Irritable Bowel Syndrome (IBS). The study aim was to assess the response rate of weekly symptom reports via Short Message Service (SMS). The subjects were undergraduates in a private medical university in Malaysia. They were identified through a previous university wide study as suffering from IBS based on Rome III criteria. The subjects were randomly assigned to either the treatment arm receiving a daily probiotic, or the placebo arm. They were required to score their symptoms using eight-item-questionnaires at baseline, and thereafter weekly, for a total of 8 weeks. All subjects were given the choice to communicate their symptom scores by text messaging via mobile phones or by email. SMS text messages were sent to remind trial subjects to attend face-to-face visits and to complete a paper based 34-item-questionnaires on IBS quality of life assessment at baseline and at end of 8 weeks.
Findings
The response rate of weekly symptom scores via Short Message Service (SMS) from a total of 38 subjects was 100%. Through the study, 342 reports were submitted: 33.3% of these were received on the due date without reminder, 60.0% one day after the deadline, after a single reminder, 6.1% 2-3 days after the deadline, after 2-3 reminders and 0.6% 5 days after the deadline, after SMS, phone reminder and face-to-face encounter. All SMS symptom reports, whether on time or late, were complete. With the help of SMS reminder, all trial subjects completed the paper based IBS quality of life assessment at baseline and at end of study.
Conclusions
This study found using text messaging via mobile phone an excellent instrument for collecting weekly symptom reports in response to trial medication, reminding trial subjects to attend face to face visits and completing more complex paper based evaluation. The 100% response rate of weekly symptom reports was facilitated by using simple number codes for SMS submission.
Trial Registration
Not appropriate.
doi:10.1186/1756-0500-3-342
PMCID: PMC3022815  PMID: 21172018
17.  Genetic adult lactase persistence is associated with risk of Crohn's Disease in a New Zealand population 
BMC Research Notes  2010;3:339.
Background
Mycobacterium avium subspecies paratuberculosis (MAP) is an infective agent found in ruminants and milk products, which has been suggested to increase the risk of gastrointestinal inflammation in genetically susceptible hosts. It is hypothesized that lactase persistence facilitates exposure to such milk products increasing the likelihood of adverse outcomes. Individuals either homozygous or heterozygous for the T allele of DNA variant, rs4988235, located 14kb upstream from the LCT locus, are associated with having lactase persistence.
The aim of this study was to determine whether lactase persistence as evident by the T allele of rs4988235 is associated with Crohn's Disease (CD) in a New Zealand population.
Findings
Individuals homozygous for the T allele (T/T genotype) showed a significantly increased risk of having CD as compared with those homozygous for the C allele (OR = 1.61, 95% CI = 1.03-2.51). Additionally, a significant increase in the frequency of the T allele was observed in CD patients (OR = 1.30, 95% CI = 1.05-1.61, p = 0.013), indicating that the T allele encoding lactase persistence was associated with an increased risk of CD.
Conclusions
Our findings indicate that lactase persistence as evident by the presence of the T allele of rs4988235 is associated with risk of CD in this New Zealand Caucasian population.
doi:10.1186/1756-0500-3-339
PMCID: PMC3020180  PMID: 21167073
18.  Social capital and self-rated health among adolescents in Brazil: an exploratory study 
BMC Research Notes  2010;3:338.
Background
Social capital may influence health and the patterns of association differ according its dimension such as cognitive, behavioral, bridging or bonding. There is a few numbers of studies in Latin America which comprise these aspects of social capital and health. The aim of this study was to examine the association between social capital and self-rated health among youth, and distinguish between the different forms of social capital - cognitive versus behavioral, and bonding versus bridging.
Findings
A cross-sectional study was conducted in 2009 among working adolescents supported by a Brazilian NGO. The sample comprised 363 individuals and data were collected using a validated structured questionnaire. The outcome, self-rated health, was measured as a dichotomous variable (poor/good health) and fourteen social capital indicators were investigated (cognitive, behavioral and bonding/bridging). Data were analyzed using multivariate logistic regression. Cognitive (social support and trust), behavioral (civic participation) and bridging social capital were associated with good self-rated health after adjustment of all the other social capital indicators and confounders (sex, age, skin color and educational background).
Conclusions
Social capital was associated with self-rated health and the patterns of association differed according its specific dimensions. Cognitive, behavioral and bridging social capitals were protective for adolescents health living in a developing country context..
doi:10.1186/1756-0500-3-338
PMCID: PMC3014966  PMID: 21162730
19.  MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing 
BMC Research Notes  2010;3:337.
Background
Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation.
Findings
MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper.
Conclusions
The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org.
doi:10.1186/1756-0500-3-337
PMCID: PMC3012040  PMID: 21159174
20.  Trial protocol and preliminary results for a cluster randomised trial of behavioural support versus brief advice for smoking cessation in adolescents 
BMC Research Notes  2010;3:336.
Background
Many young people report they want to stop smoking and have tried to do so, but most of their quit attempts fail. For adult smokers, there is strong evidence that group behavioural support enhances quit rates. However, it is uncertain whether group behavioural support enhances abstinence in young smokers trying to quit.
Findings
A cluster randomised trial for young people trying to stop smoking to compare the efficacy of a school-based 9 week intensive group behavioural support course versus a school-based 7 week brief advice only course. Participants were assessed for evidence of tobacco addiction and nicotine replacement therapy (NRT) was used if it was deemed appropriate by the therapist. Both types of course aimed to recruit approximately one hundred participants from approximately ten schools.
The primary outcome was successful quitting at 4 weeks after quit day judged according to the Russell standard. Had the trial been completed, abstinence at 6 months after quit day and the relationships between successful quit attempts and 1) psychological assessments of dependence prior to quitting 2) salivary cotinine concentration prior to quitting and 3) sociodemographic characteristics would also have been assessed. The proportion of participants who stopped smoking in each arm of the trial were compared using Chi square tests.
The trial was stopped shortly after it had started because funding to support the therapists running the stop smoking group behavioural support programme was withdrawn. Only three stop smoking courses were completed (two group support courses and one brief advice pharmacotherapy course). Seventeen participants in total entered the trial. At the end of the courses, one participant (10%) attending the group support programme had stopped smoking and no participant attending the brief advice programme had stopped smoking.
Discussion
The trial was stopped so we were unable to determine whether group support helped more young people to stop smoking than brief advice. Engagement and recruitment of participants proved much more difficult than had been anticipated. Fifteen of the seventeen participants reported that quitting smoking was either pretty important or very important to them. Thus, the stop smoking success rate could, nevertheless, be considered disappointing.
Trial registration
Current Controlled Trials ISRCTN25181936
doi:10.1186/1756-0500-3-336
PMCID: PMC3022813  PMID: 21156068
21.  Quality control of the sheep bacterial artificial chromosome library, CHORI-243 
BMC Research Notes  2010;3:334.
Background
The sheep CHORI-243 bacterial artificial chromosome (BAC) library is being used in the construction of the virtual sheep genome, the sequencing and construction of the actual sheep genome assembly and as a source of DNA for regions of the genome of biological interest. The objective of our study is to assess the integrity of the clones and plates which make up the CHORI-243 library using the virtual sheep genome.
Findings
A series of analyses were undertaken based on the mapping the sheep BAC-end sequences (BESs) to the virtual sheep genome. Overall, very few plate specific biases were identified, with only three of the 528 plates in the library significantly affected. The analysis of the number of tail-to-tail (concordant) BACs on the plates identified a number of plates with lower than average numbers of such BACs. For plates 198 and 213 a partial swap of the BESs determined with one of the two primers appear to have occurred. A third plate, 341, also with a significant deficit in tail-to-tail BACs, appeared to contain a substantial number of sequences determined from contaminating eubacterial 16 S rRNA DNA. Additionally a small number of eubacterial 16 S rRNA DNA sequences were present on two other plates, 111 and 338, in the library.
Conclusions
The comparative genomic approach can be used to assess BAC library integrity in the absence of fingerprinting. The sequences of the sheep CHORI-243 library BACs have high integrity, especially with the corrections detailed above. The library represents a high quality resource for use by the sheep genomics community.
doi:10.1186/1756-0500-3-334
PMCID: PMC3020178  PMID: 21144002
22.  Morphological analysis of the sheathed flagellum of Brucella melitensis 
BMC Research Notes  2010;3:333.
Background
It was recently shown that B. melitensis is flagellated. However, the flagellar structure remains poorly described.
Findings
We analyzed the structure of the polar sheathed flagellum of B. melitensis by TEM analysis and demonstrated that the Ryu staining is a good method to quickly visualize the flagellum by optical microscopy. The TEM analysis demonstrated that an extension of the outer membrane surrounds a filament ending by a club-like structure. The ΔftcR, ΔfliF, ΔflgE and ΔfliC flagellar mutants still produce an empty sheath.
Conclusions
Our results demonstrate that the flagellum of B. melitensis has the characteristics of the sheathed flagella. Our results also suggest that the flagellar sheath production is not directly linked to the flagellar structure assembly and is not regulated by the FtcR master regulator.
doi:10.1186/1756-0500-3-333
PMCID: PMC3017070  PMID: 21143933
23.  High dietary salt does not significantly affect plasma 25-hydroxyvitamin D concentrations of Sprague Dawley rats 
BMC Research Notes  2010;3:332.
Background
The Dahl salt-sensitive rat, but not the Dahl salt-resistant rat, develops hypertension and hypovitaminosis D when fed a high salt diet. Since the salt-sensitive rat and salt-resistant rat were bred from the Sprague Dawley rat, the aim of this research was to test the hypothesis that salt-resistant and Sprague Dawley rats would be similar in their vitamin D endocrine system response to high salt intake.
Findings
Sprague Dawley, salt-sensitive, and salt-resistant rats were fed high (80 g/kg, 8%) or low (3 g/kg, 3%) salt diets for three weeks. The blood pressure of Sprague Dawley rats increased from baseline to week 3 during both high and low salt intake and the mean blood pressure at week 3 of high salt intake was higher than that at week 3 of low salt intake (P < 0.05). Mean plasma 25-hydroxyvitamin D concentrations (marker of vitamin D status) of Sprague Dawley, salt-sensitive, and salt-resistant rats were similar at week 3 of low salt intake. Mean plasma 25-hydroxyvitamin D concentrations of Sprague Dawley and salt-resistant rats were unaffected by high salt intake, whereas the mean plasma 25-hydroxyvitamin D concentration of salt-sensitive rats at week 3 of high salt intake was only 20% of that at week 3 of low salt intake.
Conclusions
These data indicate that the effect of high salt intake on the vitamin D endocrine system of Sprague Dawley rats at week 3 was similar to that of salt-resistant rats. The salt-sensitive rat, thus, appears to be a more appropriate model than the Sprague Dawley rat for assessing possible effects of salt-sensitivity on vitamin D status of humans.
doi:10.1186/1756-0500-3-332
PMCID: PMC3018403  PMID: 21143930
24.  Work related injuries: estimating the incidence among illegally employed immigrants 
BMC Research Notes  2010;3:331.
Background
Statistics on occupational accidents are based on data from registered employees. With the increasing number of immigrants employed illegally and/or without regular working visas in many developed countries, it is of interest to estimate the injury rate among such unregistered workers.
Findings
The current study was conducted in an area of North-Eastern Italy. The sources of information employed in the present study were the Accidents and Emergencies records of a hospital; the population data on foreign-born residents in the hospital catchment area (Health Care District 4, Primary Care Trust 20, Province of Verona, Veneto Region, North-Eastern Italy); and the estimated proportion of illegally employed workers in representative samples from the Province of Verona and the Veneto Region. Of the 419 A&E records collected between January and December 2004 among non European Union (non-EU) immigrants, 146 aroused suspicion by reporting the home, rather than the workplace, as the site of the accident. These cases were the numerator of the rate. The number of illegally employed non-EU workers, denominator of the rate, was estimated according to different assumptions and ranged from between 537 to 1,338 individuals. The corresponding rates varied from 109.1 to 271.8 per 1,000 non-EU illegal employees, against 65 per 1,000 reported in Italy in 2004.
Conclusions
The results of this study suggest that there is an unrecorded burden of illegally employed immigrants suffering from work related injuries. Additional efforts for prevention of injuries in the workplace are required to decrease this number. It can be concluded that the Italian National Institute for the Insurance of Work Related Injuries (INAIL) probably underestimates the incidence of these accidents in Italy.
doi:10.1186/1756-0500-3-331
PMCID: PMC3019162  PMID: 21143866
25.  Health professional's perceptions of and potential barriers to smoking cessation care: a survey study at a dental school hospital in Japan 
BMC Research Notes  2010;3:329.
Background
Smoking is currently accepted as a well-established risk factor for many oral diseases such as oral cancer and periodontal disease. Provision of smoking cessation care to patients with oral problems is a responsibility of health care professionals, particularly dentists and dental hygienists. This study examined the smoking-related perceptions and practices of dental school hospital-based health professionals in Japan.
Findings
A cross-sectional study design was used. The sample was formed from dentists, dental hygienists, physicians and nurses of a dental school hospital in Tokyo, Japan (n = 93, 72%). Participants were asked to complete an 11-item questionnaire assessing demographic variables and smoking history, provision of smoking cessation advice or care, attitudes about smoking cessation, and perceived barrier(s) to smoking cessation care. Eighteen percent of participants reported being current smokers and 15% reported being ex-smokers, with higher smoking rates reported by dentists compared with other health professionals (p = 0.0199). While recognizing the importance of asking patients about their smoking status, actual provision of smoking cessation advice or care by participants was relatively insufficient. Interventions such as 'assess willingness to make a quit attempt' and 'assist in quit attempt' were implemented for less than one-quarter of their patients who smoke. Non-smokers were more likely to acknowledge the need for increased provision in smoking cessation care by oral health professionals. 'Lack of knowledge and training' was identified as a central barrier to smoking cessation care, followed by 'few patients willing to quit'.
Conclusions
A need for further promotion of smoking cessation activities by the health professionals was identified. The findings also suggest that dentists and dental hygienists, while perceiving a role in smoking care, do require training in the provision of smoking cessation care to hospital patients. In order to overcome the potential barriers, it is necessary to provide staff with appropriate training and create an atmosphere supportive of smoking cessation activities.
doi:10.1186/1756-0500-3-329
PMCID: PMC3016266  PMID: 21138553

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